Issue to Register Singlet Recombinants that shall be not be removed by usher (starting from 2024-7-2 to 2024-09-24) [Part II]

[aviczhl2]

https://github.com/sars-cov-2-variants/lineage-proposals/issues/991 Part I https://github.com/sars-cov-2-variants/lineage-proposals/issues/1675 Part II https://github.com/sars-cov-2-variants/lineage-proposals/issues/2086 Part III

Successor issue of https://github.com/sars-cov-2-variants/lineage-proposals/issues/991

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.

As github only displays 60 comments at the same time for each issue, better refresh this issue for every 60 comments so that searching for specific recomb is easier.

@FedeGueli @AngieHinrichs @ryhisner @NkRMnZr @JosetteSchoenma @corneliusroemer

[Mydtlwn]

I think it would be better to replace issues regularly every one to three months, with the expiration date and initiation date clearly marked in the title of each issue.

[aviczhl2]

EPI_ISL_19229374, HV.1/anything recomb.

[NkRMnZr]

EPI_ISL_19234639, XBB.2.3/JN.1 recomb, bp between spike_253 to 346

[aviczhl2]

EPI_ISL_19231824, JN.1/XBB.1.16

[FedeGueli]

EPI_ISL_19254616 this is a quite interesting recombinant between LB.1 and an undesignated KR.1 + S:F59S with Orf1a:C3419Y.

https://nextstrain.org/fetch/genome-test.gi.ucsc.edu/trash/ct/subtreeAuspice2_genome_test_273ec_e17080.json?c=gt-S_59&gmax=25384&gmin=21563

It exchanged S:S31del with S:F59S confirming somewhat the observation of @ryhisner about incompatibility between 31del and S:59X

[aviczhl2]

EPI_ISL_19229782, KS.1/KP.3.1.1

This is already on tree, no need to register, just reminder.

[FedeGueli]

19259353 very recent From Mexico LB.1.3.1 with JN.1.7 resulting in a Full Quad JN.1 spike plus S:E1150D !

[aviczhl2]

EPI_ISL_19263582, LF.1.1.1/MG.1 with additional S:F59S and S:E654A.

[aviczhl2]

EPI_ISL_19264846, it has a JN.1+S;F456L spike but other places seems invovling complex recomb pattern. Some unique mutations are added on so unlikely pure contam.

[aviczhl2]

EPI_ISL_19261040, JN.1+S:F456L,Q493E spike with a unique Orf1ab that involves recomb.

[ryhisner]

EPI_ISL_19266767

LB.1.2/KP.3.2 recombinant with S:L335S collected June 26 in Utah, USA. It has R346T and Q493E, so the breakpoint is somewhere between those, most likely between 22858-23038. The only other KP.3 with C28657T from North America—including one from Colorado, a US state that borders Utah—are all KP.3.2, which has C22858T, which is absent from this sequence. The only three sequences with the same ORF1a:∆1023-1026 collected in the past four months are all LB.1.2 from the US—two collected in Utah and one in Ohio.

[FedeGueli]

EPI_ISL_19261040

there were two JN.1.4 with that Orf1b from Italy too back in early 2024, so likely that is the donor (EPI_ISL_18831265)

[aviczhl2]

EPI_ISL_19261040

there were two JN.1.4 with that Orf1b from Italy too back in early 2024, so likely that is the donor (EPI_ISL_18831265)

https://nextstrain.org/fetch/genome-test.gi.ucsc.edu/trash/ct/subtreeAuspice1_genome_test_26393_73ed10.json?f_userOrOld=uploaded%20sample&label=id:node_6250736

It seems that the initial JN.1.4 is already is a recomb with early variants prior to XBB, and then it further recombs with KP/ JN.1.16+Q493E.

@corneliusroemer @ryhisner @JosetteSchoenma what do you think of this branch?

[aviczhl2]

EPI_ISL_19267875, HK.3 recombs with sth. on Orf1ab.

[aviczhl2]

EPI_ISL_19283607, LP.3 recombs with some JN.1+S:K182E+S:F456L Spike. It doesn't have S:S31del but have other LP.3-definings.

[NkRMnZr]

EPI_ISL_19304943 looks like XBB* and KP.3.3 recomb

[aviczhl2]

EPI_ISL_19304947, EG.5.1.1/JN.1+S:F456L

[FedeGueli]

mm the last ones from SKorea both with the same little NTD switch and i think me or others have already posted some above similar to thse ones. i tend to think they are all artifacts.

[Over-There-Is]

EPI_ISL_19284930 EG.5.1.6*/JN.1 15935\~16342 JN.1> C27434T(Orf7a:T14I)> T24406G> G3692T(ORf1a:V1143F), T24951C(S:I1130T)

[NkRMnZr]

EPI_ISL_19264602 and EPI_ISL_19334658, KP.3.1.1 and (most likely) JN.1.18+S:F59S recomb gaining F59S and R346T while losing JN.1.11.1's hallmark C7113T, G17334T and KP.3.3.1's G15543T

[FedeGueli]

EPI_ISL_19339136 LB.1.3/Kp.3.3 recombinant got 5'end from LB.1 till 456-493, it has 183H 346T 493E 1104L . It is GBW from Poland Tree:

https://nextstrain.org/fetch/genome-test.gi.ucsc.edu/trash/ct/subtreeAuspice42_genome_test_27cee_265a70.json?c=userOrOld&label=id:node_11605762&s=hCoV-19/USA/CA-GBW-GKISBBBD24653/2024%7CEPI_ISL_19339136%7C2024-08-07

It is placed by Usher in the branch just below the XEC one.

[aviczhl2]

EPI_ISL_19269396, XDV.1/KP.1.2

[aviczhl2]

EPI_ISL_19351744, KP.1.1.1/LB.1.2

[FedeGueli]

there should be a KP.3.2/LB.1.7+C24421T sublineage that got the S2 from this LB.1.7 branch reverting S:V1104L and adding C24421T. Interestingly it has got also a Sotrovimab known escape mutation with S:E340Q:

https://nextstrain.org/fetch/genome-test.gi.ucsc.edu/trash/ct/subtreeAuspice1_genome_test_5a6e6_e4b0a0.json?c=userOrOld&label=id:node_7038399 Query: T12244C ,T22292C, C24421T, Samples: 4 (3 w 340Q) IDs:EPI_ISL_19272373, EPI_ISL_19353170, EPI_ISL_19353178, EPI_ISL_19357751

[aviczhl2]

there should be a KP.3.2/LB.1.7+C24421T sublineage that got the S2 from this LB.1.7 branch reverting S:V1104L and adding C24421T. Interestingly it has got also a Sotrovimab known escape mutation with S:E340Q: https://nextstrain.org/fetch/genome-test.gi.ucsc.edu/trash/ct/subtreeAuspice1_genome_test_5a6e6_e4b0a0.json?c=userOrOld&label=id:node_7038399 Query: T12244C ,T22292C, C24421T, Samples: 4 (3 w 340Q) IDs:EPI_ISL_19272373, EPI_ISL_19353170, EPI_ISL_19353178, EPI_ISL_19357751

Please make a separate issue?

[FedeGueli]

there should be a KP.3.2/LB.1.7+C24421T sublineage that got the S2 from this LB.1.7 branch reverting S:V1104L and adding C24421T. Interestingly it has got also a Sotrovimab known escape mutation with S:E340Q: https://nextstrain.org/fetch/genome-test.gi.ucsc.edu/trash/ct/subtreeAuspice1_genome_test_5a6e6_e4b0a0.json?c=userOrOld&label=id:node_7038399 Query: T12244C ,T22292C, C24421T, Samples: 4 (3 w 340Q) IDs:EPI_ISL_19272373, EPI_ISL_19353170, EPI_ISL_19353178, EPI_ISL_19357751

Please make a separate issue?

Done thx: https://github.com/sars-cov-2-variants/lineage-proposals/issues/1942

[FedeGueli]

Not sure if this is LB.1 +22N or just a recombinant with XEC maybe : https://nextstrain.org/fetch/genome-test.gi.ucsc.edu/trash/ct/subtreeAuspice2_genome_test_3de05_f92a70.json?label=id:node_11619450

[aviczhl2]

Not sure if this is LB.1 +22N or just a recombinant with XEC maybe : https://nextstrain.org/fetch/genome-test.gi.ucsc.edu/trash/ct/subtreeAuspice2_genome_test_3de05_f92a70.json?label=id:node_11619450

It doesn't have 31del, shall be recombinant.

[FedeGueli]

Not sure if this is LB.1 +22N or just a recombinant with XEC maybe : https://nextstrain.org/fetch/genome-test.gi.ucsc.edu/trash/ct/subtreeAuspice2_genome_test_3de05_f92a70.json?label=id:node_11619450

It doesn't have 31del, shall be recombinant.

Thank you! right i have not thought at that!

[aviczhl2]

EPI_ISL_19332182, MB.1.1/undesignated KP.2.3+S:T572I, it gets additional S:K478T rev.

[NkRMnZr]

a weird cluster reverting BA.2.86's synonymous C25207T/S:Y1215Y also having some spike diversity already, unsure if recomb involved, just drop it here with query: T3160A, A13121T, G21800T

https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice25_genome_1a12c_d72d50.json?label=id:node_7131106

Edit: transferred to #2019

[FedeGueli]

LK.2.1/JN.1.11.1.X recombinant losing Orf1a:P>H3395Y and taking Orf1a:T2283I 3 samples EPI_ISL_19386820 EPI_ISL_19386817 EPI_ISL_19386819

https://nextstrain.org/fetch/genome-test.gi.ucsc.edu/trash/ct/subtreeAuspice1_genome_test_3cafd_199bf0.json?label=id:node_7275732

[aviczhl2]

EPI_ISL_19407493, XDV.1/JN.1

[FedeGueli]

a weird cluster reverting BA.2.86's synonymous C25207T/S:Y1215Y also having some spike diversity already, unsure if recomb involved, just drop it here with query: T3160A, A13121T, G21800T

https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice25_genome_1a12c_d72d50.json?label=id:node_7131106

This is getting big, even if only a canadian cluster it is going on adding spike mutation , very interesting please propose it

Spike Mutations: S:D80Y, S:K440R Query: T3160A, A13121T, G21800T Samples: 19 Country : 1 Canada

https://nextstrain.org/fetch/genome-test.gi.ucsc.edu/trash/ct/subtreeAuspice1_genome_test_5baa1_1fa030.json?label=id:node_7133705

Please @NkRMnZr propose it

[Over-There-Is]

hCoV-19/South_Korea/KDCA295278/2024|EPI_ISL_19411567|2024-08-21 potential JN.1.11.1/XBB.1.9.2

[aviczhl2]

EPI_ISL_19410817, JN.1.11.1/KS.1

[FedeGueli]

Jn.1.4.5/LB.1.3 recombinant : EPI_ISL_19409479 Tree:

https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_b9f_82a280.json?label=id:node_7113730

[FedeGueli]

Weird # 2774-XEC-alike recombinant sample having Orf1a:S4286C and C12616T maybe a further recombinant? : EPI_ISL_19413561

https://nextstrain.org/fetch/genome-test.gi.ucsc.edu/trash/ct/subtreeAuspice4_genome_test_56317_be12f0.json?label=id:node_7053962

Edited it has not S:S31del , now corrected, sorry.

first spotted by @ryhisner

[NkRMnZr]

EPI_ISL_19418214 another XEC-like recomb https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice21_genome_42ba3_bf5570.json?label=id:node_11656883

[FedeGueli]

JN.1.7.3/KP.2 recombinant with S:S31del and S:S704L: EPI_ISL_19424789

[aviczhl2]

EPI_ISL_19430030, XDV.1.7/BA.2.86?

[aviczhl2]

EPI_ISL_19430120, XDV.1/BA.2.86?

[FedeGueli]

EPI_ISL_19430030

with also S:A1174V

[FedeGueli]

There could be a recombinant between JN.1.7 and KP* with S:T22N Query: T13954C ,C7113T, C21627A Samples: 17 Tree:

https://nextstrain.org/fetch/genome-test.gi.ucsc.edu/trash/ct/singleSubtreeAuspice_genome_test_379f6_1f7e40.json?f_userOrOld=uploaded%20sample&label=id:node_7288113

I am unsure if 22N was inherited by JN.1.7 or by some KP* + 22N

[aviczhl2]

There could be a recombinant between JN.1.7 and KP* with S:T22N Query: T13954C ,C7113T, C21627A Samples: 17 Tree: https://nextstrain.org/fetch/genome-test.gi.ucsc.edu/trash/ct/singleSubtreeAuspice_genome_test_379f6_1f7e40.json?f_userOrOld=uploaded%20sample&label=id:node_7288113

I am unusre if 22N was inherited by JN.1.7 or by some KP* + 22N

It doesn't have reversions and C7113T is very convergent, I think it shall be separate emergence as they lack G17334T.

[FedeGueli]

I am unsure if 22N was inherited by JN.1.7 or by some KP* + 22N

mm looking at the tree ,not downsampled, it could have been also convergent evolution: https://nextstrain.org/fetch/genome-test.gi.ucsc.edu/trash/ct/subtreeAuspice1_genome_test_379f6_1f7e40.json?label=id:node_7297284

[aviczhl2]

I am unsure if 22N was inherited by JN.1.7 or by some KP* + 22N

mm looking at the tree ,not downsampled, it could have been also convergent evolution: https://nextstrain.org/fetch/genome-test.gi.ucsc.edu/trash/ct/subtreeAuspice1_genome_test_379f6_1f7e40.json?label=id:node_7297284

Yeah you can make an issue for the S:F456L sub-branch. It seems recent.

[FedeGueli]

I am unsure if 22N was inherited by JN.1.7 or by some KP* + 22N

mm looking at the tree ,not downsampled, it could have been also convergent evolution: https://nextstrain.org/fetch/genome-test.gi.ucsc.edu/trash/ct/subtreeAuspice1_genome_test_379f6_1f7e40.json?label=id:node_7297284

Yeah you can make an issue for the S:F456L sub-branch. It seems recent.

also in the branch below there is a recent seq from Canada with weird S:F2L mutation

[FedeGueli]

Yeah you can make an issue for the S:F456L sub-branch. It seems recent.

thx for helping now proposed in #2083

[aviczhl2]

EPI_ISL_19430317, JN.1.13/XDV.1.3