JN.1.4 on T18453C branch with ORF1a:W646L (nsp2_W466L), ORF1a:L3919F (nsp7_L60F), ORF1a:K4348R (nsp10_K95R), ORF1b:E2266I (nsp15_E215I, triple nuc), S:R346T, S:F456L and S:S477D (7 seqs, El Salvador and USA)

[NkRMnZr]

Defining Mutations: JN.1.4 > T18453C > C5284T > T22928C(S:F456L) > G22599C(S:R346T) > _T5284Crev > A13308G(ORF1a:K4348R) > C313T, G2202T(ORF1a:W646L), C12020T(ORF1a:L3919F), G20263A, A20264T, A20265T(ORF1b:E2266I), A22991G(S:S477D, or S>N477D over existing G22992A), G27441A, T29008C Query: C12020T, A22991G Earliest seq: 2024-06-28 (EPI_ISL_19254700, ex. El Salvador) Latest seq: 2024-07-29 (EPI_ISL_19343112, Utah, USA) Sampled Countries: USA (4: FL/1; UT/1; 2 GBW sample ex. El Salvador)

Genomes:

for `lineages.csv` commit: ``` USA/FL-CDC-QDX21693125/2024 USA/UT-UPHL-240816796406/2024 USA/VA-GBW-GKISBBBD38944/2024 USA/CA-GBW-GKISBBBD17514/2024 ``` epi_isl accessions: `EPI_ISL_19254700, EPI_ISL_19307732, EPI_ISL_19343112`

UShER: https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_1691b_ddbcd0.json?label=id:node_7173931

Trivia:

• It is placed like a side-branch to XED on UShER (without XED's S31Δ, probably misplacement), not sure if it's a convergent addition of S:R346T and S:F456L to JN.1.4 or another recombination.
• A triple-nuc mutation ORF1b:E2266I (nsp15_E215I) / G20263A, A20264T, A20265T sampled about 400 times during the whole pandemic
• Two-nuc mutation S:S477D (or S:S>N477D) sampled about 1000 times during the whole pandemic
• It could also have S:G181V (G22104T), the only seqs without it is the GBW sample with Ns around.

[xz-keg]

The 5284 is a FLip-FLop reversion thing @AngieHinrichs, is it possible to fix it?

[AngieHinrichs]

The placement near XED is interesting -- could this also be a recombinant? Here is a view of the larger branch in the 2024-08-28 tree (black-circled node is this branch, blue-circled node is the reversion of 5284 after FLiRT mutations, XED at the bottom is truncated):

The 5284 is a FLip-FLop reversion thing @AngieHinrichs, is it possible to fix it?

Only one sequence (USA/OH-ODH-SC4031568/2024) ties in the sequences with FLiRT and without 5284T (including this branch and XED). But the two FLiRT mutations have a stronger pull than just 5284 (or its absence), and I don't see a plain old JN.1.4+FLiRT branch with no other mutations. So I think even if I try a prune & replace with that one sequence, it probably still wouldn't fix it. Chalk it up to recurring mutations making it hard for parsimony to build the right tree. Thanks @NkRMnZr for highlighting the flip-flop.

[FedeGueli]

One more sequence from August from California

[FedeGueli]

clsoing this

[FedeGueli]

6 but no recent samples closing for now

[NkRMnZr]

there are a few seqs not on GISAID yet: USA/FL-CDC-QDX21693125/2024|PQ212309.1|2024-08-01, USA/CA-CDC-QDX23211369/2024|PQ363473.1|2024-09-04 but it doesn't seem to be fast

[NkRMnZr]

no new seqs