JN.1.3+S:F456L with Orf8:Q18* (16 seqs)

cov-lineages / pango-designation

Repository for suggesting new lineages that should be added to the current scheme

Other

1.04k stars 97 forks source link

JN.1.3+S:F456L with Orf8:Q18* (16 seqs) #2655

Closed DailyCovidCases closed 1 month ago

DailyCovidCases commented 3 months ago

From branch 25 of https://github.com/sars-cov-2-variants/lineage-proposals/issues/1253 JN.1.3+S:F456L Query: T3565C,T22928C,C27945T,-C4777T No. of seqs: 96 usher Screenshot (113)

FedeGueli commented 3 months ago

ping @corneliusroemer this is very interesting it has Orf8:Q18* and then 456L and then 190S:

https://nextstrain.org/fetch/genome-test.gi.ucsc.edu/trash/ct/subtreeAuspice2_genome_test_5fd27_eb3700.json?c=gt-S_456&gmax=25384&gmin=21563&label=id:node_6945828

Query for the S:R190S branch (the one that is still around): C2156T, G18079A, A20486C Samples:10 EPI_ISL_18847465, EPI_ISL_18878653, EPI_ISL_18878658, EPI_ISL_18885936, EPI_ISL_18931712, EPI_ISL_19146012, EPI_ISL_19146014, EPI_ISL_19162530, EPI_ISL_19162533, EPI_ISL_19164065

thx @DailyCovidCases

FedeGueli commented 3 months ago

Btw 27945T corresponds to Orf8:Q18* please add it to the title @DailyCovidCases

DailyCovidCases commented 3 months ago

307 seqs with Orf8:Q18* now

FedeGueli commented 3 months ago

i see 62, can you check?

FedeGueli commented 3 months ago

How can you find the correct query of this issue?. I used this website: nextclade I type JN.1.3+S:F456L and it says 0 sequences!

Try orf8:Q18*, S:456L, T3565C,

DailyCovidCases commented 3 months ago

It still says there are 0 sequences! Maybe your query is incorrect

FedeGueli commented 3 months ago

don't add JN.1.3 and you will get (click)

Anyway and more important this lineage got S:R190S

So the proposal should be edited: JN.1.3> T22928C> ORF1a:L631F (C2156T) Orf1b:V1538I (G18079A), S:R190S (G22132T), C26907T, T29689C Query: C2156T, G18079A, G22132T

Samples: 17

Please edit the proposal

Ping @corneliusroemer this is quite interesting Tree:

https://nextstrain.org/fetch/genome-test.gi.ucsc.edu/trash/ct/subtreeAuspice1_genome_test_2a0a7_a700.json?label=id:node_6945677

DailyCovidCases commented 2 months ago

Tracked in tracker25 Is it worth to be designated? @corneliusroemer

DailyCovidCases commented 1 month ago

Tree now: usher Screenshot (168)

FedeGueli commented 1 month ago

All the recent samples are from other lineages it is no more monophyletic:

https://nextstrain.org/fetch/genome-test.gi.ucsc.edu/trash/ct/singleSubtreeAuspice_genome_test_5958_dd85d0.json?f_userOrOld=uploaded%20sample&label=id:node_6948800

DailyCovidCases commented 1 month ago

This lineage are no longer monophyletic. Closing this.