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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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KR.1 (FLiRT) got S:F59S (110, >10 countries including Philippines and Japan) with a branch with S:A435S,S:S680P (12, South Korea,US) #2681

Closed FedeGueli closed 2 weeks ago

FedeGueli commented 4 months ago

transferred from https://github.com/sars-cov-2-variants/lineage-proposals/issues/1670

KR.1 > S:F59S (T21738C) >> ORF1a:C3419Y (G10521A),G29543T then>>C16675T > A13318G, T22054C (S:N164N), S:A435S (G22865T) Query: C28498T ,T22928C,C1762A,T21738C Samples: 89 Countries: 10 mainly Philippines (where it likely emerged), Japan, California, South Korea, Canada , Australia With a branch, spotted by @aviczhl2 , carrying two additional spike mutations S:A435S and S:S680P Query for the 435S branch: C16675T,A13318G, T22054C Samples: 8 (S.Korea,US)

Tree:

Screenshot 2024-09-01 alle 14 53 59

https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_256e7_4632b0.json?f_userOrOld=uploaded%20sample&label=id:node_7171824 Tree for the 435S branch:

Screenshot 2024-09-01 alle 14 54 39

IDs EPI_ISL_19162486, EPI_ISL_19162527, EPI_ISL_19189341, EPI_ISL_19190117, EPI_ISL_19191455, EPI_ISL_19192899, EPI_ISL_19195692, EPI_ISL_19199242, EPI_ISL_19208173, EPI_ISL_19210931, EPI_ISL_19220364, EPI_ISL_19220372, EPI_ISL_19222088, EPI_ISL_19226740, EPI_ISL_19227262, EPI_ISL_19230901, EPI_ISL_19230975-19230976, EPI_ISL_19230992, EPI_ISL_19232851, EPI_ISL_19232854, EPI_ISL_19233915, EPI_ISL_19238872, EPI_ISL_19241332, EPI_ISL_19245124, EPI_ISL_19245126, EPI_ISL_19245195, EPI_ISL_19251028, EPI_ISL_19251504, EPI_ISL_19257384, EPI_ISL_19257904-19257905, EPI_ISL_19258078, EPI_ISL_19258109, EPI_ISL_19258125, EPI_ISL_19261935, EPI_ISL_19263205, EPI_ISL_19264232, EPI_ISL_19266193, EPI_ISL_19273928, EPI_ISL_19274080, EPI_ISL_19282963, EPI_ISL_19282975, EPI_ISL_19299317, EPI_ISL_19302444, EPI_ISL_19302508, EPI_ISL_19304264, EPI_ISL_19304438, EPI_ISL_19304445, EPI_ISL_19304547, EPI_ISL_19304552, EPI_ISL_19304723, EPI_ISL_19304726, EPI_ISL_19306374, EPI_ISL_19306531, EPI_ISL_19309917, EPI_ISL_19311314, EPI_ISL_19314099, EPI_ISL_19314124, EPI_ISL_19314130, EPI_ISL_19314142, EPI_ISL_19314162, EPI_ISL_19314167, EPI_ISL_19314173, EPI_ISL_19314197, EPI_ISL_19314226, EPI_ISL_19314228, EPI_ISL_19314237, EPI_ISL_19314264, EPI_ISL_19317263, EPI_ISL_19326019, EPI_ISL_19332576, EPI_ISL_19340508, EPI_ISL_19340562, EPI_ISL_19340803, EPI_ISL_19344202, EPI_ISL_19345455, EPI_ISL_19346312, EPI_ISL_19347664, EPI_ISL_19352517, EPI_ISL_19352641, EPI_ISL_19354461, EPI_ISL_19358645, EPI_ISL_19360437, EPI_ISL_19367497, EPI_ISL_19368928, EPI_ISL_19368946, EPI_ISL_19369006, EPI_ISL_19369009,

FedeGueli commented 2 months ago

I ve reopened it here after @aviczhl2 spotted a sublineage of interest with 435S

Ping @corneliusroemer

FedeGueli commented 1 month ago

97/11 i think this could be designated likely circulated much more than what we see from seqs count.

DailyCovidCases commented 1 month ago

Now 100 seqs. Tree now: usher Tracked in issue2681 Screenshot (213) ping @corneliusroemer Is this branch worth a designation?

DailyCovidCases commented 1 month ago

This branch has slowed down a lot. You can close this.

FedeGueli commented 1 month ago

Lets wait a bit more, S Korea is slow to upload ,

FedeGueli commented 1 month ago

104 none recent closing it

FedeGueli commented 1 month ago

One more from S Korea in September

DailyCovidCases commented 2 weeks ago

Slowing down closing it

FedeGueli commented 1 week ago

designated KR.1.4 via https://github.com/cov-lineages/pango-designation/commit/73becf76eb345c5a843bd52f97a137acd0742c56