Closed krosa1910 closed 5 months ago
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.
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.
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.
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.
please propose it.
The first find by @ryhisner in cov-lineages/pango-designation/issues/2426
322 now
Likely dead
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