XDE/JN.1/XDE recombinant (14 sequences from USA, China, & Germany)

[emily-smith1]

There is only one sequence so far, but this is worth monitoring as we know that JN.1 has a clear growth advantage worldwide. ORF1ab appears to be GW.5*, Spike is JN.1, and N/ORF9b are likely XBB.1.9* due to the presence of ORF9b:I5T and absence of N:Q229K (thanks to @ryhisner for help determining this).

Description

Earliest sequence: 2023-11-09
Most recent sequence: 2023-11-09
Countries circulating: USA-CA
GISAID query: C1170T,C6501A,T22926C

Genomes

EPI_ISL_18576372

Evidence

[xz-keg]

Was discussed in sars-cov-2-variants/lineage-proposals#991, it seems that the donor is XDE,

[Over-There-Is]

Let's wait for the next sequences and check 29535 site. It could be an XDE/JN.1 sandwich recombinant.

[FedeGueli]

@corneliusroemer it is the one you posted in # 991 other repo yesterday morning.

[emily-smith1]

The above GISAID nucleotide query does now identify a second genome (EPI_ISL_18651234), but it has many AA substitutions in ORF1a and ORF1b that differentiate it from the first. I'm hesitant to say these are the same recombinant without more data. I think we would also expect more localized spread in USA-CA if this were truly growing. This other genome is from Singapore but a traveler from Saudi Arabia, collected 2023-12-06.

[xz-keg]

The above GISAID nucleotide query does now identify a second genome (EPI_ISL_18651234), but it has many AA substitutions in ORF1a and ORF1b that differentiate it from the first. I'm hesitant to say these are the same recombinant without more data. I think we would also expect more localized spread in USA-CA if this were truly growing. This other genome is from Singapore but a traveler from Saudi Arabia, collected 2023-12-06.

That one is a recombinant of GW.5.3.1 and JN.1.

[xz-keg]

+1 for the XDE/JN.1 recomb in the proposal.
Suggest to change query to C1170T,C6501A,T22926C,T28297C

EPI_ISL_18750362

This one doesn't have 29535 too, so maybe the donor is not XDE but something unknown.

[xz-keg]

+1 more for this. 18778665

@AngieHinrichs It seems that they are still not on usher tree despite I add them to recombinants.tsv.

The donor is not XDE though. It is GW.5/JN.1/XBB.1+Orf9b:I5T through unknown middle steps, as 29535 is bonded to XDE in it's FL.13.4.1 donor.

[FedeGueli]

3 in tot

[xz-keg]

+2 EPI_ISL_18837291 and EPI_ISL_18837421

[FedeGueli]

Scratch unrelated

[AngieHinrichs]

@AngieHinrichs It seems that they are still not on usher tree despite I add them to recombinants.tsv.

Ah, there were two different places where I needed to make filtering of long paths less stringent, not just one. This was being added to the tree every day but then was filtered out. It should be fixed in tomorrow's build, 2024-01-31. Thanks for pointing it out @aviczhl2!

[xz-keg]

One more sample, 18869745

[xz-keg]

9 seqs now

[alantsangmb]

Could XDE still be the donar for them (XDE+JN.1 recombinant), considering that they possess the C7113T (XDE) but lack the C29535T (JN.1)? The potential breakpoint lies between 19326 and 213363.

[xz-keg]

C1170T,C6501A,T22926C,T28297C

This one is dead anyway.

Could XDE still be the donar for them (XDE+JN.1 recombinant), considering that they possess the C7113T (XDE) but lack the C29535T (JN.1)? The potential breakpoint lies between 19326 and 213363.

It can be a 3-BP XDE/JN.1 recomb though, with 3rd BP before 29535.

Given there exist other clear 3-BP recombs now. sars-cov-2-variants/lineage-proposals#1428 We shall take 3-BP into consideration.

[xz-keg]

+1 Hong Kong with additional S:F456L(T22930A)

[Over-There-Is]

+1 Hong Kong with additional S:F456L.

and this sequence has no private mutations sharing with other sequences.

[Over-There-Is]

breakpoints:
19326~21608
27915~28297
28958~29535
no private mutation

[xz-keg]

+1 Gansu, China. with additional S:G504D

[xz-keg]

breakpoints: 1932621608 2791528297 28958~29535 no private mutation

yeah, more likely a 3-BP XDE/JN.1 recomb.

[xz-keg]

+2 GBW from Hong Kong, with the same T22930A-S:F456L of the Hong Kong local seq.

[xz-keg]

@corneliusroemer suggest to designate this. correct query: C1170T,C6501A,T22926C,T28297C

[xz-keg]

One more Germany seq from the S:F456L branch

[corneliusroemer]

Indeed looks like a single XDE/JN.1/XDE recombinant - interestingly the 456L is T22930A, which is a lot rarer than T22928C - there's not a single designated JN.1 lineage yet with 22930A as opposed to 22928C

This suggests that 456L was acquired on top of the original recombinant - as opposed to through an independent recombination even involving XDE and a 456L JN.1 sublineage

Ignore the 541 split, they all have 541 - this is a branch specific masking artefact

https://nextstrain.org/fetch/genome-test.gi.ucsc.edu/trash/ct/subtreeAuspice1_genome_test_35ba1_bed970.json?branchLabel=nuc%20mutations&label=id:node_6996075

[xz-keg]

Indeed looks like a single XDE/JN.1/XDE recombinant - interestingly the 456L is T22930A, which is a lot rarer than T22928C - there's not a single designated JN.1 lineage yet with 22930A as opposed to 22928C

This suggests that 456L was acquired on top of the original recombinant - as opposed to through an independent recombination even involving XDE and a 456L JN.1 sublineage

It lacks the XDE-defining 29535(which is from its FL.13.4.1 donor), so has to be XDE/JN.1/XDE/JN.1, 3 breakpoints.

[corneliusroemer]

Right! It could be either reversion, or 3 breakpoints, or an extra XBB ORF9b:5T donor involved, or reversion of 29535

Lots of options, luckily not really relevant for designation, other than having something reasonable in lineage notes

[corneliusroemer]

And there's another one: hCoV-19/Australia/NSW-ICPMR-53316/2024|EPI_ISL_19027110|2024-03-18

Now designated as XDV (this issue) and XDV.1 (with 456L)

[FedeGueli]

Now there is one with 346T > FLiRT : EPI_ISL_19110341

https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_2f846_b70840.json?f_userOrOld=uploaded%20sample

it has three reversions: G6183A, T9142C, C13339T

cc @aviczhl2 not sure if it could be a recombinant with some JN.1 + Orf1a:L3116F