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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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JN.1.1+S:S31F+S:R346T(Designated LC.1)+S:F456L(3 seqs, 2 countries) #2490

Closed xz-keg closed 7 months ago

xz-keg commented 9 months ago

From https://github.com/sars-cov-2-variants/lineage-proposals/issues/1157

JN.1.1+C21654T(S:S31F)

GISAID query: C21654T,C11747T,C1762A,-9142,-19011,-14070 No. of seqs: 51(Australia 1 Austria 1 Canada 2 Dominician Republic 4 France 1 India 10 Israel 2 UK 1 Singapore 2(2 from China) South Korea 1 Spain 3 Switzerland 1 USA 22(1 from Australia))

First: EPI_ISL_18445258, 2023-10-23, Singapore from China Latest: EPI_ISL_18886466, 2024-2-2, USA from Australia

Query for S:R346T branch: C21654T,C1762A,G22599C (9 seqs) Query for S:F456L further branch: C21654T,C1762A,G22599C,T22928C (3 seqs)

There is also a C9142T branch under this. However the correct order of that one shall be JN.1.1+C9142T+S:S31F. So that one is excluded in query.

Some seqs are placed elsewhere due to artefact reversions. They shall belong to this branch.

usher

image

FedeGueli commented 9 months ago

10 with 346T, Illinois +1

xz-keg commented 8 months ago

Designated JN.1.1.7

xz-keg commented 8 months ago

Continue tracking the S:R346T branch, now 10 seqs from USA, India, Austria and Australia(via GBW)

FedeGueli commented 8 months ago

Continue tracking the S:R346T branch, now 10 seqs from USA, India, Austria and Australia(via GBW)

it is also branch 40 in # 1089

designated via https://github.com/cov-lineages/pango-designation/commit/e312db588d211527e101812a04f602fb6874e2fd

xz-keg commented 8 months ago

14, Japan(via GBW)

There is an additional S:F456L branch for this. Added in description.

FedeGueli commented 8 months ago

14, Japan(via GBW)

There is an additional S:F456L branch for this. Added in description.

Yeah it is also Branch 40 of # 1089

xz-keg commented 7 months ago

Designated LC.1

xz-keg commented 7 months ago

The S:F456L sub-branch seems no seq since 2024-3-15, close this.

FedeGueli commented 7 months ago

https://github.com/cov-lineages/pango-designation/commit/dffbf6a1afdaf756b5644c1b76c25f2953260210