Issue to Register Singlet Recombinants that shall be not be removed by usher (starting from 2024-12-5 ) Part IV.

[xz-keg]

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

Successor issue of #2086

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 ~50 comments at the same time for each issue, better refresh this issue for every 50 comments so that searching for specific recomb is easier.

[xz-keg]

19606872,19606873,19606893, 3 more samples of a previous KP.2.1/BA.5* recombinant, all from Tasmania maybe same patient.

[FedeGueli]

|EPI_ISL_19616806 Recombinant betweeen LB.1.2.2 + KP.3

[xz-keg]

EPI_ISL_19616296, complex LF.7 recombinant that loses K444R and gains Q493E. Hard to tell the other donor.

[FedeGueli]

EPI_ISL_19618600 XEC/ ? recombinant it kept 22N losing 59S and gaining 31del
https://nextstrain.org/fetch/genome-test.gi.ucsc.edu/trash/hgPhyloPlace/subtreeAuspice1_genome_test_53961_8878c0.json?label=id:node_7266832

[ryhisner]

There's a GBW sequence that's an LP.8.1.1/LF.7 recombinant. Mostly LP.8.1.1, but it switched out its NTD for LF.7's. Got T22N, S31P, and K182R. Lost F186L. Also has H207Y.

It's a traveler from Ethiopia, so it's possible this could be more widespread in Africa.

EPI_ISL_19644736

[FedeGueli]

Ethiopia
cc @ryhisner
great catch! maybe better proposing it as singlet in the secondary repo it could be something

[FedeGueli]

LB.1.3.1 with Kp.3 that exchanged 445P for 445H+493E

EPI_ISL_19659582

https://nextstrain.org/fetch/genome-test.gi.ucsc.edu/trash/hgPhyloPlace/subtreeAuspice47_genome_test_4a424_13e6a0.json?label=id:node_7184083

[FedeGueli]

19662239 likely recombinant between LP.8.1 and A KP.2.2.1 WITH S:E654Q BPI between S: 494-653

[FedeGueli]

There is a LF.7.1/XEN recombinant in Wales:
Query: C3170A, C6195T,T3565C
https://nextstrain.org/fetch/genome-test.gi.ucsc.edu/trash/hgPhyloPlace/subtreeAuspice1_genome_test_3ce0ed_eb70f0.json?label=id:node_11863028

[Over-There-Is]

USA/VA-VCUVAS3-JWPN910963/2025|EPI_ISL_19704015|2025-01-26 KP.3.1.1*/XEC.8

edited: tree: https://nextstrain.org/fetch/genome-test.gi.ucsc.edu/trash/hgPhyloPlace/subtreeAuspice1_genome_test_1538f3_5cbde0.json
Query: C2947T,C2450T, A7040G,T3565C

[FedeGueli]

EPI_ISL_19712226 is LF.7.1/XEF recombinant with breakpoint after LF.7.1 NTD
https://nextstrain.org/fetch/genome-test.gi.ucsc.edu/trash/hgPhyloPlace/subtreeAuspice1_genome_test_dc760_72aa00.json
Query:C4993T,G4694A,C4891T

[FedeGueli]

This should be a XDY/XDV.1 recombinant in Finland 4 samples:
Query:T28297C, C22858T, C29108T,C11001T

https://nextstrain.org/fetch/genome-test.gi.ucsc.edu/trash/hgPhyloPlace/subtreeAuspice1_genome_test_32806c_b5b4e0.json?label=id:node_11867245

[xz-keg]

T28297C, C22858T, C29108T,C11001T

It is #2291

[FedeGueli]

EPI_ISL_19712226 is LF.7.1/XEF recombinant with breakpoint after LF.7.1 NTD https://nextstrain.org/fetch/genome-test.gi.ucsc.edu/trash/hgPhyloPlace/subtreeAuspice1_genome_test_dc760_72aa00.json Query:C4993T,G4694A,C4891T

One more of this now from Singapore proposing it

[FedeGueli]

19718651 recombinant XEQ/MC.30.1.1
Query:T22822C, G22865T, C23277T, T18375C

BPI between 21740 and 22597

https://nextstrain.org/fetch/genome.ucsc.edu/trash/hgPhyloPlace/subtreeAuspice1_genome_2a8c61_c6baf0.json?label=id:node_7183574

[FedeGueli]

EPI_ISL_1972376 should be a complex MC.31/XEC or an artifact:
https://nextstrain.org/fetch/genome.ucsc.edu/trash/hgPhyloPlace/subtreeAuspice1_genome_18c8b_e6b7b0.json?c=userOrOld&label=id:node_7325410

[FedeGueli]

EPI_ISL_19724626 from Quebec:
Another LF.7 recombinant that got 445R 487D 493E 572I likely from a LP.8.1.2 donor
Two Breakpoints at S:444 and Between S:494 and S:1085
Query:T4214C, T8350C,C29409T,T3565C
https://nextstrain.org/fetch/genome.ucsc.edu/trash/hgPhyloPlace/subtreeAuspice2_genome_1f28a7_efd270.json

[Over-There-Is]

EPI_ISL_1972376 should be a complex MC.31/XEC or an artifact: https://nextstrain.org/fetch/genome.ucsc.edu/trash/hgPhyloPlace/subtreeAuspice1_genome_18c8b_e6b7b0.json?c=userOrOld&label=id:node_7325410

EPI_ISL_19723764