New JN.1.18 FLiRT lineage with S:L492L and Orf6:I60T likely emerged in Africa (16) with one S:K182I sublineage (6 seqs), one with S:F1103S (3) and another one with S:I197V,P251H (2seqs)

[FedeGueli]

Original proposal
Formerly tracked as Branch 87 of sars-cov-2-variants/lineage-proposals#1089

JN.1.18 (S:R346T)> S:F456L (T22930G), T23036C (Silent:S:L492L) , Orf6:I60T (T27380C) thx @aviczhl2 for noting the right placement .
Query: T27380C,T22930G
Samples: 5 ( 6 on Usher) with one sample from Ethiopia and one from Ghana
EPI_ISL_19029565, EPI_ISL_19062760, EPI_ISL_19070234,
EPI_ISL_19075644, EPI_ISL_19075660
I want to highlight that silent mutation S:L492L (T23036C) could open up a way to 492P/Q/R if 23037 will mutate further

Tree:

There are two branches:
One with S:K182I
[defining #2567 >>Orf1a:G604S (G2075A), S:K182I (A22107T) ]
query: G2075A, A22107T, T27380C
Samples: 3

One with S:I197V (A22151G), S:P251H
#2567 > ORF1a:E1766A (A5562C),C9565T, T16950C S:I197V (A22151G), S:P251H (C22314A), C27247T
Query: C9565T, T16950C ,A22151G
Samples: 2

One with S:F1103S
#2567 > S:F1103S (T24870C)
Query: T24870C,T27380C
Samples: 3 (NY), (Ca)

[FedeGueli]

8 now , the last two GBW (likely same patient) samples have two additional spike mutations: S:I197V and S:P251H

[FedeGueli]

10 growing

[FedeGueli]

@AngieHinrichs now this has been misplaced under the Branch 20 of sars-cov-2-variants/lineage-proposals#1253 but i think it is very hard to think it belongs really there cause this has T22930G while Branch 20 is the collector of everything with T22930A ( in the same way Jn.1.16 did for T22928C)

cc @corneliusroemer @aviczhl2

[aviczhl2]

The 27143 branch is errorous and usher has fixed it. This one shall be sub-branch of JN.1.18

[FedeGueli]

The 27143 branch is errorous and usher has fixed it. This one shall be sub-branch of JN.1.18

Thx!

[AngieHinrichs]

@AngieHinrichs now this has been misplaced under the Branch 20 of sars-cov-2-variants/lineage-proposals#1253 but i think it is very hard to think it belongs really there cause this has T22930G while Branch 20 is the collector of everything with T22930A ( in the same way Jn.1.16 did for T22928C)

Yes, UShER and/or matOptimize is placing it wrong there. Thanks for the reminder, I need to make a simple test case for a bug report.

[FedeGueli]

@AngieHinrichs now this has been misplaced under the Branch 20 of sars-cov-2-variants/lineage-proposals#1253 but i think it is very hard to think it belongs really there cause this has T22930G while Branch 20 is the collector of everything with T22930A ( in the same way Jn.1.16 did for T22928C)

Yes, UShER and/or matOptimize is placing it wrong there. Thanks for the reminder, I need to make a simple test case for a bug report.

Thank you!