JN.1.1+S:R346T mini saltation branch with S:L455S->A, S:31del and ORF7a:T28I (3 seqs in Singapore and Malaysia)

[HynnSpylor]

Defining mutations:
EDITED : JN.1.1+C9442T > C5407A,C27476T,G22599C,T22925G,del21653_21655
[ original proposal :JN.1.1.7>G22599C (S:R346T)>C5407A, C9442T, T22925G (S:L455S->A), C27476T (ORF7a:T28I)]

GISAID query: C5407A, T22925G, C27476T
Earliest seq: 2024-03-18 (Malaysia, EPI_ISL_19025958)
Most recent seq: 2024-03-25(Singapore, EPI_ISL_19033217)
Countries detected: Singapore (2), Malaysia (1)

Usher Tree: (Notice that the S:K484E rev is common artefact in Singapore)

https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_16ce3_3578d0.json

It is a small saltation branch from JN.1.1.7+S:R346T sublineage. As S:L455S achieves great success recently, there is still few S:L455F (for XBB* FLip) and S:L455A (for some JN.1* seq S:L455S->A).
We can monitor the new branch for a time.

Genomes:
EPI_ISL_19025958, EPI_ISL_19033217, EPI_ISL_19033219

[xz-keg]

That's not JN.1.1.7. They have S:S31del instead of the JN.1.1.7-defining S:S31F.

[xz-keg]

The real path shall be
JN.1.1+C9442T+C5407A,C27476T,G22599C,T22925G,del21653_21655

There may also be a recombinant event with JN.1.8.2 that may explain 2 mutations, C27476T,G22599C

[FedeGueli]

The real path shall be JN.1.1+C9442T+C5407A,C27476T,G22599C,T22925G,del21653_21655

There may also be a recombinant event with JN.1.8.1 that may explain 2 mutations, C27476T,G22599C

JN.1.8.2

[FedeGueli]

if the path is the one propose by @HynnSpylor this is a LC.1 sublineage , please check if placement have been modified

[xz-keg]

if the path is the one propose by @HynnSpylor this is a LC.1 sublineage , please check if placement have been modified

Nope. This one has S:31-, not 31F.

[FedeGueli]

if the path is the one propose by @HynnSpylor this is a LC.1 sublineage , please check if placement have been modified

Nope. This one has S:31-, not 31F.

i ve modified the defining mutations accordingly

[xz-keg]

No more seqs