Issue to Register Singlet Recombinants that shall be not be removed by usher ( Until 2024-7-2 ) [Part I]

[xz-keg]

#991 Part I
#1675 Part II
#2086 Part III

I'd like to post this issue to help everyone propose any recombinant sequence that may be added to usher.

Anything with >5 reversion(refer to the last checkpoint ,usually a designation) or >20 private mutations(distance to the last node) may be removed by usher. However some of them are real recombinants.

There are quite a few recombinants meeting this criteria. Whenever you happen to see any of them, please register them here to help those recombinant singlets not becoming invisible, hence when a 2nd seq appears we may easily realize the cluster.

Even if you are unsure about recomb or artefact please submit. It may be artefact but having 1 more artefact seq on tree doesn't harm as much as missing a real recomb.

XCM and XCT are both discovered this way so it shall be very meaningful.

Registered recombinants will be added to recombinants.tsv so that they won't be dropped out by usher.

@FedeGueli @AngieHinrichs @ryhisner @NkRMnZr @JosetteSchoenma

[JosetteSchoenma]

@aviczhl2 You say removed by Usher. But what will I see in Usher if I run a fasta of such samples through it?
Do you mean that it will be put on the wrong branch while showing reversions?

[FedeGueli]

@aviczhl2 You say removed by Usher. But what will I see in Usher if I run a fasta of such samples through it? Do you mean that it will be put on the wrong branch while showing reversions?

XZ is referring to the fact that unless you don't upload the fasta Usher won't show it cause it excludes sequences with too many reversions as default

[JosetteSchoenma]

@aviczhl2 You say removed by Usher. But what will I see in Usher if I run a fasta of such samples through it? Do you mean that it will be put on the wrong branch while showing reversions?

XZ is referring to the fact that unless you don't upload the fasta Usher won't show it cause it excludes sequences with too many reversions as default

Oke. So, if I do upload one and it has more than 5 reversions or more then 20 private mutations, report it here. Is that it? Will that not put a lot of chronics here as well?

[FedeGueli]

@aviczhl2 You say removed by Usher. But what will I see in Usher if I run a fasta of such samples through it? Do you mean that it will be put on the wrong branch while showing reversions?

XZ is referring to the fact that unless you don't upload the fasta Usher won't show it cause it excludes sequences with too many reversions as default

Oke. So, if I do upload one and it has more than 5 reversions or more then 20 private mutations, report it here. Is that it? Will that not put a lot of chronics here as well?

You should have hints of recombination. If reversions are sparse and don't make you think to a recombinant no need to put it into the list

[FedeGueli]

I ve pinned this on the homepage so easy to get it

[AngieHinrichs]

From my point of view, it would be ideal if you could add them to the new file that @corneliusroemer just added:

https://github.com/sars-cov-2-variants/lineage-proposals/blob/main/recombinants.tsv

I have set up my build to automatically spare (from the too-many-reversions filter) any sequences that are listed there (name must include the ID, for example I parse "EPI_ISL_18076084" out of the name "France/GES-IPP16300/2023|EPI_ISL_18076084|2023-07-10"). That is a bit more work than commenting in an issue, but it means that there is no waiting until I have time to add them to my local file! The tab-separated format has the nice table-formatted display in github too, which is nicer for tracking than searching through issue comments.

You would need write access to the sars-cov-2-variants/lineage-proposals repo, but I think everybody on this thread can be trusted with that. :)

The singletons with more than 20 private mutations will still be pruned, there is not currently a way to exempt particular sequences from that filter operation. I can raise it to 25 -- the more time that passes, the more divergence is to be expected.

[xz-keg]

Register one here.
EPI_ISL_18416021, Looks like an XCT(or its parent in #811)/#972(or its DV.7.1-donor) recomb. The XCT donor has additional S:151R.

Breakpoint between 24074 and 27506.

usher

[FedeGueli]

GK.1/XBB.1.16 https://t.co/CqYJWeNLlr
https://nextstrain.org/fetch/genome-test.gi.ucsc.edu/trash/ct/subtreeAuspice1_genome_test_6380b_b81730.json

Epi_Isl_18421965 singlet

[ryhisner]

There may already be an issue for this, but there's a JY.1/XBB.1.16.24 recombinant branch with 11 sequences. It's XBB.1.16* from ORF7a to the 3' end, and the rest is JY.1. It also has S:N641S and ORF1a:S2535L, which seem to be exclusive to this recombinant.
Query: C5173T, T2552C, C29386T

[FedeGueli]

There may already be an issue for this, but there's a JY.1/XBB.1.16.24 recombinant branch with 11 sequences. It's XBB.1.16* from ORF7a to the 3' end, and the rest is JY.1. It also has S:N641S and ORF1a:S2535L, which seem to be exclusive to this recombinant. Query: C5173T, T2552C, C29386T

There is no proposal for it please do it

[JosetteSchoenma]

Singlet EPI_ISL_18440692 HK.3/JN.1 Spike from JN.1

#1024

[JosetteSchoenma]

Not completely sure if this belongs here, but EG.5.1/XBB.1.16. Close to XCV in the tree. 4 samples
3 from Switzerland, not on GISAID, one from the Netherlands on GISAID EPI_ISL_18441654

[FedeGueli]

Dubious recombinant between JC.2/HV.1 : EPI_ISL_18438637 : https://nextstrain.org/fetch/genome-test.gi.ucsc.edu/trash/ct/subtreeAuspice1_genome_test_135a5_c17110.json?c=gt-S_339&gmax=25384&gmin=21563

[xz-keg]

EPI_ISL_18443676, looks like recombinant of #1016(HK.3+L452M) and GK.2.1

[FedeGueli]

18443676

It has also S:L517F if another one pops up please propose it.

[xz-keg]

EPI_ISL_18450958, looks like recomb of XBB.1.16 and GK.3.1

[JosetteSchoenma]

HF.1.1/BA.2.86.1 recombinant
Singlet England EPI_ISL_18450393
#1040

[FedeGueli]

Member

It seems a sandwich XBB.1.16/GK.3.1/XBB.1.16
but be aware that Germany ENV samples showing recombinants sometimes are instead contaminations

[xz-keg]

EPI_ISL_18455278

EG.5.1(likely EG.5.1.4)/XCT recomb

[xz-keg]

EPI_ISL_18443676, looks like recombinant of #1016(HK.3+L452M) and GK.2.1

EPI_ISL_18462697 belongs to the same branch

Try to make a query: C15755G, C22916A

[xz-keg]

It has also S:L517F if another one pops up please propose it.

Another one pops up but does not have S:L517F.

[FedeGueli]

It has also S:L517F if another one pops up please propose it.

Another one pops up but does not have S:L517F.

propose it the same if they are the same recombinant.

[FedeGueli]

EPI_ISL_18378307 is a JG.3.1/XBB.1.16.15/JG.3.1/XBB.1.16.15/JG.3 putative recombinant most likely to me contamination/coinfection:
https://cov-spectrum.org/explore/World/AllSamples/Past6M/variants?nucMutations=T12730A%2CC29625T%2C2059G%2C14856A&nextcladePangoLineage=XBB.1.16.15*&nextcladePangoLineage1=JG.3.1*&nextcladePangoLineage2=XBB.1.16.15*&analysisMode=CompareEquals&

[FedeGueli]

This JN.1.4 FLirt branch could be instead one or multiple recombinants with JN.1.16.1:

https://nextstrain.org/fetch/genome-test.gi.ucsc.edu/trash/ct/subtreeAuspice13_genome_test_59a3e_335390.json?label=id:node_7107236

[xz-keg]

This JN.1.4 FLirt branch could be instead one or multiple recombinants with JN.1.16.1: https://nextstrain.org/fetch/genome-test.gi.ucsc.edu/trash/ct/subtreeAuspice13_genome_test_59a3e_335390.json?label=id:node_7107236

I think that's just JN.1.4-FLiRT, JN.1.4+C5284T+FLiRT and JN.1.4.5+FLiRT misplaced together.

[FedeGueli]

I think that's just JN.1.4-FLiRT, JN.1.4+C5284T+FLiRT and JN.1.4.5+FLiRT misplaced together.

it has also s:31del

[FedeGueli]

I think that's just JN.1.4-FLiRT, JN.1.4+C5284T+FLiRT and JN.1.4.5+FLiRT misplaced together.

it has also s:31del

More samples of this:

https://nextstrain.org/fetch/genome-test.gi.ucsc.edu/trash/ct/subtreeAuspice25_genome_test_4216a_564680.json?c=userOrOld&label=id:node_12207460

the three samples with 1263l and 31del to me are very likely recombinants between JN.1.4 and LF.1.1.1

[xz-keg]

the three samples with 1263l and 31del to me are very likely recombinants between JN.1.4 and LF.1.1.1

Yeah, that 3 looks quite possible recombs.
Others are JN.1.4-FLiRT, JN.1.4+C5284T+FLiRT and JN.1.4.5+FLiRT and JN.1.4.5+C28948T+FLiRT misplaced together.

[FedeGueli]

the three samples with 1263l and 31del to me are very likely recombinants between JN.1.4 and LF.1.1.1

Yeah, that 3 looks quite possible recombs. Others are JN.1.4-FLiRT, JN.1.4+C5284T+FLiRT and JN.1.4.5+FLiRT and JN.1.4.5+C28948T+FLiRT misplaced together.

yeah i agree. sorry i wasnt cler in the first tweet, i ve looked at those sequences, but as usual around recombinants usher tree could place other possible recombinants, that i was meaning.

[xz-keg]

EPI_ISL_19203296, EG.5.1/JN.1+S:F456L. It seems to have some other interesting mutations, S:E132Q, H146K, D178H, A688V, S704P, H1058Y and K1073N

[FedeGueli]

EPI_ISL_19203296, EG.5.1/JN.1+S:F456L. It seems to have some other interesting mutations, S:E132Q, H146K, D178H, A688V, S704P, H1058Y and K1073N

great catch this is super interesting one better to specify it :

It has also S:P9L the mutation analyzed by @ryhisner multiple times,
but it got also the NTD from EG.5.1 with further mutations, the RBD from JN.1+456L, from the end of Rbd to 3'end from EG.5.1 with multiple N mutations

https://nextstrain.org/fetch/genome-test.gi.ucsc.edu/trash/ct/subtreeAuspice1_genome_test_4ba9a_807780.json?f_userOrOld=uploaded%20sample

ping @corneliusroemer @ryhisner

Suggested query: C14980T, C21588T,C8860T

[FedeGueli]

potential recombinant between KP.2.3 and LB.1+31del?: EPI_ISL_19214475 with S:N405N T22777C

https://nextstrain.org/fetch/genome-test.gi.ucsc.edu/trash/ct/subtreeAuspice2_genome_test_24d0e_a90570.json?c=userOrOld

not sure of it

[FedeGueli]

A side branch of XDV appeared, i think it is unrelated or a recombinant of XDV. @aviczhl2 @JosetteSchoenma could you take a look at it:

https://nextstrain.org/fetch/genome-test.gi.ucsc.edu/trash/ct/subtreeAuspice15_genome_test_4d139_eed9e0.json?f_userOrOld=uploaded%20sample&label=id:node_11503430

EPI_ISL_19221357,EPI_ISL_19221366

[JosetteSchoenma]

A side branch of XDV appeared, i think it is unrelated or a recombinant of XDV. @aviczhl2 @JosetteSchoenma could you take a look at it: https://nextstrain.org/fetch/genome-test.gi.ucsc.edu/trash/ct/subtreeAuspice15_genome_test_4d139_eed9e0.json?f_userOrOld=uploaded%20sample&label=id:node_11503430

EPI_ISL_19221357,EPI_ISL_19221366

EPI_ISL_19221357 is the red line here and EPI_ISL_19221366 from China is the one just above it.
I think the red one is just rubbish and the Chinese one is just on a branch with a few extra mutations.
I searched for C9996R, C1884T and A21137G, which besides these 2 also found the XBB.1.5 at the bottom, which does not seem related.

[xz-keg]

A side branch of XDV appeared, i think it is unrelated or a recombinant of XDV. @aviczhl2 @JosetteSchoenma could you take a look at it: https://nextstrain.org/fetch/genome-test.gi.ucsc.edu/trash/ct/subtreeAuspice15_genome_test_4d139_eed9e0.json?f_userOrOld=uploaded%20sample&label=id:node_11503430
EPI_ISL_19221357,EPI_ISL_19221366

EPI_ISL_19221357 is the red line here and EPI_ISL_19221366 from China is the one just above it. I think the red one is just rubbish and the Chinese one is just on a branch with a few extra mutations. I searched for C9996R, C1884T and A21137G, which besides these 2 also found the XBB.1.5 at the bottom, which does not seem related.

19221366 is XDV.1 with Orf1a:L3829F, Orf1b:K2557R , two famous beneficial non-spike mutations.
19221357 seems to be GBW pooled sample involving XDV.1
@ryhisner what do you think?

[JosetteSchoenma]

I think it is likely that the 357 is pooled, both because of what it looks like and because there is no originating country given.

[xz-keg]

I think it is likely that the 357 is pooled, both because of what it looks like and because there is no originating country given.

AAA is pooled (like H10) and BBB is personal (like H20)

[JosetteSchoenma]

I think it is likely that the 357 is pooled, both because of what it looks like and because there is no originating country given.

AAA is pooled (like H10) and BBB is personal (like H20)

Oke. It's AAA so pooled. So, why did you say it that it seemed pooled and ask for Ryan's opinion, if you know that?

[ryhisner]

I agree with everyone's thoughts.

It's really frustrating how GBW's pooled samples end up screwing up the Usher Tree. I've been criticizing them for doing pooled samples at every opportunity, but apparently no one cares. GBW has been paid over $100 million now to do this sequencing, and they can't even be bothered to follow the most basic rules. What a pathetic state of affairs.

[xz-keg]

Oke. It's AAA so pooled. So, why did you say it that it seemed pooled and ask for Ryan's opinion, if you know that?

Pooled are not always artifacts though. Most of them are actually the same as the BBB seq. Only when 2 travelers infected by different variants mixed in one pool is troublesome.

[FedeGueli]

Ok thanks i ve looked mostly to the non pooled one and that row of reversions made me think it could have been a further recombinant.Thank you for your time

[JosetteSchoenma]

Ok thanks i ve looked mostly to the non pooled one and that row of reversions made me think it could have been a further recombinant.Thank you for your time

I didn't see any reversions.

[xz-keg]

Ok thanks i ve looked mostly to the non pooled one and that row of reversions made me think it could have been a further recombinant.Thank you for your time

That's an usher bug on recombinants. @AngieHinrichs

Is it possible to remove those fixed positions on recombinant branches(at least for designated recombs)?

[FedeGueli]

Thx again Il sab 29 giu 2024, 08:54 Xu Zou ***@***.***> ha scritto:

…

Ok thanks i ve looked mostly to the non pooled one and that row of reversions made me think it could have been a further recombinant.Thank you for your time That's an usher bug on recombinants. @AngieHinrichs <https://github.com/AngieHinrichs> — Reply to this email directly, view it on GitHub <#991 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AU43YNJ5PN2YHFLGMJNKJTLZJZK3JAVCNFSM6AAAAAA6IGJT3KVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDCOJYGAYTOOJTGY> . You are receiving this because you were mentioned.Message ID: ***@***.***>

[xz-keg]

EPI_ISL_19216679, BA.2.12.1/?

[FedeGueli]

EPI_ISL_19224177 LA.1/KP.3 recomb

[xz-keg]

EPI_ISL_19224596, XDQ.1 recombs with other XBB-3' variants and lose its 28846.

[xz-keg]

Github seems to be displaying 60 comments at the same time. I think it's better refresh this long-term issue for every 60 comments. I'll close this one and create a new one.