JN.1+2-nuc Orf1b:I2273S(65 seqs, 13 countries, 35 with S:R346T, 27 with additional S:F456L)

[xz-keg]

There seems to be a 2-nuc mutation under JN.1.

JN.1+T20285C,A20284T(Orf1b:I2273S)

GISAID query: T20285C, A20284T, C18894T,-13584,-1762,-C774T,-29684,-12781,-17334
No. of seqs: 41(Brazil 2 Canada 1 Costa Rica 6 UK 6 France 2 Germany 1 Guatemala 1 Ireland 1 Mexico 1 China 2 Sweden 5 USA 13(4 from Mexico, 2 from UK))
GISAID query for S:R346T branch: T20285C, A20284T, C18894T, G22599C,-17334 (8 seqs)
GISAID query for S:R346T+S:F456L branch: T20285C, A20284T, C18894T, G22599C,T22928C,-17334 (2 seqs)

First: EPI_ISL_18534932, Canada, 2023-11-6
Latest: EPI_ISL_19026930, Sweden, 2024-3-7

usher

[ryhisner]

This is a probable TRS-L recombination mutation that sometimes is accompanies by ORF1b:E2274K, which makes the TRS-L match more extensive.

There was a sequences from Costa Rica recently—probably one of the sequences on this branch—that had another 2-nuc mutation in addition to ORF1b:I2273S.

[FedeGueli]

Thx very good catch added as branch 90 of #1089 to try to keep che tglobal picture there (unsure if possible for long time then)

[FedeGueli]

Now 46 /10/ 3 i suggest to propose it also due it is widespread in three central american countries

[FedeGueli]

49/12/5 pls propose it

[xz-keg]

Some convergent ones are separated by usher now. Correct toll shall be 40.

[FedeGueli]

48 now with 20 with r346T and 13 with FLiRT , please propose it @aviczhl2

[FedeGueli]

Ps the last FLiRT ones has got S:T95I too.

https://nextstrain.org/fetch/genome-test.gi.ucsc.edu/trash/ct/subtreeAuspice5_genome_test_22ce3_ce35f0.json?label=id:node_7039850

[FedeGueli]

51 tot +1 Flirt please propose it

[FedeGueli]

All the samples with N:A134V from Sweden has S:S31del and are tracked as branch 8 of #1502 , today one unrelated appeared with S:R346S (not in the flirt branch) ans S:S31del too. It doesnt seem to be something to track at this point. just a recall if more pops up.

[FedeGueli]

@aviczhl2 propose this one please.

[FedeGueli]

24 for the FLirt sublineage pls propose it.

[FedeGueli]

27 i would restrict the proposal to the FLiRT one being the only one still circulating

[xz-keg]

27 i would restrict the proposal to the FLiRT one being the only one still circulating

Sure

[FedeGueli]

85 seqs now

when closed we updated in the transferred issue # 2679

[DailyCovidCases]

93 seqs now, 74 with Orf1ab:I6674S please propose it @aviczhl2
https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/singleSubtreeAuspice_genome_30c22_7a12e0.json?f_userOrOld=uploaded%20sample

[FedeGueli]

93 seqs now, 74 with Orf1ab:I6674S please propose it @aviczhl2 https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/singleSubtreeAuspice_genome_30c22_7a12e0.json?f_userOrOld=uploaded%20sample

It is already proposed