JN.1.48+S:F456L branches, JN.1.48.1 and Sibling branch of JN.1.48.1 with Orf3a:S60F (28 seqs, 10 countries)

[aviczhl2]

From branch 50 of https://github.com/sars-cov-2-variants/lineage-proposals/issues/1253

There a very recent FLiRT+S:S60P lineage growing very rapidly. After some investigation it seems quite complex.

JN.1+T18471C+C25688T(Orf3a:A99V)+T3913A+C8092T, T21740C, G22599C, C25378T(S:S60P,R346T) +T22928C(S:F456L)

GISAID query: C25378T, G22599, C8092, T21740 No. of seqs: 6(USA 5(2 from India), UK 1)

First: EPI_ISL_18874336, 2024-1-24, USA-TX Latest: EPI_ISL_19028035, 2024-3-22, USA-CA

GISAID query for S:F456L branch: C25378T, G22599, T22928,C8092 (5 seqs) GISAID query for FLIRT branch: C25378T, G22599, T22928,C8092,C23277T (1 seq)

Above S:F456L branch--JN.1+Orf3a:S60F

Breakpoint between 22929 and 25377

C25378T, C25688T reverted in exchange for C25571T(Orf3a:S60F) Many JN.1* branches have C25571T so unable to decide the precise branch. Additional mutation: C5547T(Orf1a: T1761I), private mutation

This can also be separate S:F456L emergence under JN.1.48.

GISAID query: C25571T, C8092T,T22928C No. of seqs: 2(USA-GBW baseline survellience)

EPI_ISL_19019175, 19028032, 2024-3-21

Due to the complexity, usher isn't showing the correct mutation order.
The bottom is the recomb and the upper is the main branch. @AngieHinrichs

usher

[FedeGueli]

thanks for the analysis!

[aviczhl2]

+1 India local

[aviczhl2]

+1 USA +1 Australia There is a S:T572I FLIRT USA seq on this branch.

[FedeGueli]

+1 USA +1 Australia There is a S:T572I FLIRT USA seq on this branch.

Query for Trio : C23277T,C25378T, T3913. (the US sample has T3913W)

[aviczhl2]

13, Netherlands

[FedeGueli]

C25378T, G22599, T22928,C8092,C23277T

it seems very fast to me.

[FedeGueli]

Designated JN.1.48.1 via https://github.com/cov-lineages/pango-designation/commit/67f48bf24283999f1940f3aee8159f404124ff3f

[aviczhl2]

Designated JN.1.48.1 via 67f48bf

That's a quite ambigious designation. Does it refers to S:R346T branch, F456L further-branch, or the recomb with Orf3a: 60 instead of Orf3a:99? @corneliusroemer

Also calling @AngieHinrichs to fix the tree here. Here a recombinant is disrupting the placement of non-recombinants.

[FedeGueli]

Designated JN.1.48.1 via 67f48bf

That's a quite ambigious designation. Does it refers to S:R346T branch, F456L further-branch, or the recomb with Orf3a: 60 instead of Orf3a:99? @corneliusroemer

Also calling @AngieHinrichs to fix the tree here. Here a recombinant is disrupting the placement of non-recombinants.

after orf3a:A99V according to the line of lineage notes

[corneliusroemer]

unclear by nature of the lack of sequences so far, we'll see when more sequences come in

[AngieHinrichs]

The red circles here are designated sequences from lineages.csv and they clearly indicate this branch that has both R346T and F456L as well as two other mutations (it is downstream of the node with ORF3a:A99V):

Also calling @AngieHinrichs to fix the tree here. Here a recombinant is disrupting the placement of non-recombinants.

I don't see the problem -- can you give examples of sequence names that you think are in the wrong place? I see that there is a reversion on ORF3a:A99V in the two USA/VA-GBW sequences, and a reversion on C22928T (S:L456F) in 3 India sequences, but I don't see a way to get something better with a parsimony tree.

[aviczhl2]

The red circles here are designated sequences from lineages.csv and they clearly indicate this branch that has both R346T and F456L as well as two other mutations (it is downstream of the node with ORF3a:A99V):

Also calling @AngieHinrichs to fix the tree here. Here a recombinant is disrupting the placement of non-recombinants.

I don't see the problem -- can you give examples of sequence names that you think are in the wrong place? I see that there is a reversion on ORF3a:A99V in the two USA/VA-GBW sequences, and a reversion on C22928T (S:L456F) in 3 India sequences, but I don't see a way to get something better with a parsimony tree.

Some have S:L456F reversion or Orf3a:V99A reversion.

[aviczhl2]

The usher tree alters to be correct now, and the designation of JN.1.48.1 becomes buggy. @corneliusroemer

usher

[FedeGueli]

The usher tree alters to be correct now, and the designation of JN.1.48.1 becomes buggy. @corneliusroemer

usher

Already asked to @AngieHinrichs it should be fixed.

[aviczhl2]

Already asked to @AngieHinrichs it should be fixed.

The usher tree is correct now. The designation needs to be fixed.

[FedeGueli]

Already asked to @AngieHinrichs it should be fixed.

The usher tree is correct now. The designation needs to be fixed.

but the designation is this one: JN.1.48.1 Alias of B.1.1.529.2.86.1.1.48.1, S:S60P, S:R346T, S:F456L, after ORF3a:A99V so it should be ok isn it?

[FedeGueli]

in the mean while second sequence with FLiRTrio (346T 456L 572I) for this one

[AngieHinrichs]

@corneliusroemer There are 3 designated sequences for JN.1.48.1 that (according to the UShER tree so they might have N at 22928?) do not have S:F456L:

India/MH_BJCOG_6494/2024|EPI_ISL_19032849|2024-02-22
India/MH_BJCOG_INSACOG_6562/2024|EPI_ISL_19033124|2024-03-02
USA/TX-HMH-M-138364/2024|EPI_ISL_18874336|2024-01-24

[aviczhl2]

but the designation is this one: JN.1.48.1 Alias of B.1.1.529.2.86.1.1.48.1, S:S60P, S:R346T, S:F456L, after ORF3a:A99V so it should be ok isn it?

It now only includes the recombinant branch of 3 seqs.

[FedeGueli]

but the designation is this one: JN.1.48.1 Alias of B.1.1.529.2.86.1.1.48.1, S:S60P, S:R346T, S:F456L, after ORF3a:A99V so it should be ok isn it?

It now only includes the recombinant branch of 3 seqs.

You mean only three sequences added? Cause the commit and the lineages note are both correct.

[FedeGueli]

in the mean while second sequence with FLiRTrio (346T 456L 572I) for this one

3 now

https://nextstrain.org/fetch/genome-test.gi.ucsc.edu/trash/ct/singleSubtreeAuspice_genome_test_471cf_abe240.json?f_userOrOld=uploaded%20sample&label=id:node_6982025&s=hCoV-19/USA/MA-CDC-LC1103020/2024%7CEPI_ISL_19070143%7C2024-04-06

[aviczhl2]

but the designation is this one: JN.1.48.1 Alias of B.1.1.529.2.86.1.1.48.1, S:S60P, S:R346T, S:F456L, after ORF3a:A99V so it should be ok isn it?

It now only includes the recombinant branch of 3 seqs.

You mean only three sequences added? Cause the commit and the lineages note are both correct.

It is only 3 on usher now. It was ill-defined at that time(falsely includes wrong things because of wrong tree), and the tree changes to be correct after designation, so the designation doesn't fit the correct tree now.

[FedeGueli]

JN.1.48.1 plus S:T572I is now 5, please re-arrange the proposal to highlight it, (Query:C23277T,C25378T, T3913)

https://nextstrain.org/fetch/genome-test.gi.ucsc.edu/trash/ct/subtreeAuspice10_genome_test_2243_340e10.json?label=id:node_6989022

About the route of JN.1.48.1 i think now it is correct: JN.1>> T18471C > G29134T > Orf3a:A99V (C25688T) > T3913A > C8092T, S:S60P (T21740C), C25378T > S:S346T (G22599C) > S:f456L (T22928C) > S:T572I (C23277T )

[FedeGueli]

T572I branch now at 6

[FedeGueli]

FLIRT>TRIO BRANCH now tops 7

[FedeGueli]

Trio >> 8

[FedeGueli]

Trio branch designated LD.1 via https://github.com/cov-lineages/pango-designation/commit/426e1569bce1e55db1bcc49e40e92f962558d199

[FedeGueli]

Recomb now 12

[aviczhl2]

The recombinant is now 16 seqs in France, USA. South Africa, and GBW from Germany and Fiji.

[FedeGueli]

26

[aviczhl2]

Spain, Mexico, Jamaica and New Zealand for the recomb

[aviczhl2]

@corneliusroemer suggest to designate the recomb here. 26 seqs from 9 countries now.

[FedeGueli]

@corneliusroemer suggest to designate the recomb here. 26 seqs from 9 countries now.

agree two samples in the last GBW batch from two countries both undersampled ones.

[aviczhl2]

28,Canada

[aviczhl2]

Currently usher explains them as two separate S:F456L emergence of JN.1.48. That could be possible and hence recomb may not be the only explanation.