JN.1.4* with C21302T,C21304A,G21305A triple mutation (322 seqs, 10 countries mostly Israel at 03-26)

[krosa1910]

Mutations: JN.1.4(JN.1+C774T/Orf1a:T170I/NSP1 T170I)+,C21302T, C21304A, G21305A Notes: many, or even majority of the sequences gets T18453C, T1510C, C5784T(Orf1a:T1840I), C23628T or C28201T(orf8:S103L), but because those CT transitions are too common and most does not correspond with meaningful aa mutations so I ignore them. Gisaid Inquiry:C21302T, C21304A, G21305A,C774T,T15756A Earliest Sequence: EPI_ISL_18596536 Denmark 2023-11-20 Latest Sequence: EPI_ISL_18781263 Isarel 2024-01-08 Usher Tree: https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/singleSubtreeAuspice_genome_28c15_8d46a0.json?f_userOrOld=uploaded%20sample

nextclade result: https://clades.nextstrain.org/tree

nextclade.csv

[krosa1910]

https://github.com/sars-cov-2-variants/lineage-proposals/issues/539#issuecomment-1665909177 Ryan described the significance of this triple mutation quite well, so I would quote it from that previous issue. This branch seems to show good speed, if that is not misled by the large Isarel cluster then it probab

ly deserve designation.

[corneliusroemer]

Can you list how many are Israel and other countries? This is almost entirely Israel with so-so sequence quality so I'm a bit hesitant. It jumps a bit too fast from 0 to 20% in Israel.

[krosa1910]

C21302T, C21304A, G21305A,C774T,T15756A

3 Belgium, 2 Canada, 1 Denmark, 1 Netherlands, 1 USA, the rest Isareal, I would present a usher tree with manually marked series shortly after.

[krosa1910]

Yeah, this tree's quality is not so good, all the foreign sequences are clustered before the large Isareli clade, which is further characterized by the mutation T1510C, I would consider changing the proposal.

[FedeGueli]

please propose it.

[Memorablea]

The first find by @ryhisner in cov-lineages/pango-designation/issues/2426

[FedeGueli]

322 now

[FedeGueli]

Likely dead