Need help with weird UShER placement on a few lineages (XBB.1.5* & XBB.1.5.77 with S:T478R) (15/28 seqs)

[NkRMnZr]

Bumping into some really weird UShER (mis-)placement, starting with #305, and then #314 by @aviczhl2 , now there's another:

when I found some South African lineages with T478R, it is placed in that particular weird XBB.1.5's T17124C > T10204C > T24845C > T23018C > C24845T flip-flop branch, again:
https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_19fd4_44a010.json?c=gt-S_478&f_userOrOld=uploaded%20sample&showBranchLabels=all

however, if using query T10204C,C27005T, C22995G to try finding those seqs, which will fail to catch them, and those sequences with that query actually placed under a XBB.1.5.77's sub-branch, follows:XBB.1.5.77 > C24706T > C16575T > G10364A(ORF1a:V3367I) > C679T, G1820A(ORF1a:G519S), C12534T(ORF1a:T4090I), C22995G(S:T478R), C28567T, A29147G(N:I292V), T29515A

https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_1dfa2_44c6b0.json?f_userOrOld=uploaded%20sample

My theory is that either something wrong with UShER, or some kind of drop-out causing the issue. Could they be the same lineage, just split by good sequence and potential artifact? Or are these some kind of recombinant? I'm totally confused.

Genomes for those from South Africa (and the USA) on weird flip-flop branch, having trouble with query too

South_Africa/NICD-N55321/2023|EPI_ISL_17803355|2023-05-16
South_Africa/NICD-N55462/2023|EPI_ISL_17801595|2023-05-24
South_Africa/NICD-N55457/2023|EPI_ISL_17801590|2023-05-10
South_Africa/NICD-R00766/2023|EPI_ISL_17885142|2023-01-24
South_Africa/NICD-R00768/2023|EPI_ISL_17885140|2023-01-26
USA/AZ-CDC-QDX49328040/2023|EPI_ISL_17589852|2023-04-20
USA/CA_SACPHL_23SAC0130/2023|EPI_ISL_17738100|2023-04-24
USA/CA-HLX-STM-6G94T93CM/2023|EPI_ISL_17688448|2023-04-23
USA/FL-CDC-QDX80295151/2023|EPI_ISL_17854786|2023-05-08
USA/NV-CDC-QDX49006504/2023|EPI_ISL_17526702|2023-04-09
USA/NV-CDC-QDX49399559/2023|EPI_ISL_17621371|2023-04-22
USA/NV-CDC-QDX80338427/2023|EPI_ISL_17852406|2023-05-11
USA/TX-CDC-QDX80414718/2023|EPI_ISL_17852352|2023-05-11

many has a T insertion after 28214

Genomes on XBB.1.5.77 with S:T478R mini-saltation branch, query: C22995G, A29147G, T29515A, 15 seqs from Costa Rica & USA

CostaRica/INC-11215-793027/2023|EPI_ISL_17774089|2023-05-15
USA/CA-HLX-STM-465DV7A9F/2023|EPI_ISL_17950673|2023-06-06
USA/CA-HLX-STM-4ZZNXKJVS/2023|EPI_ISL_17950697|2023-06-06
USA/CA-HLX-STM-6J6ENP96P/2023|EPI_ISL_17950529|2023-06-01
USA/FL-CDC-LC1044327/2023|EPI_ISL_17854347|2023-06-07
USA/FL-CDC-QDX81328328/2023|EPI_ISL_17856472|2023-06-05
USA/FL-CDC-QDX81328331/2023|EPI_ISL_17856533|2023-06-06
USA/HI-H2322559/2023|EPI_ISL_17951437|2023-06-05
USA/HI-H2322625/2023|EPI_ISL_17951505|2023-06-12
USA/HI-H2322717/2023|EPI_ISL_17951589|2023-06-15
USA/TX-CDC-QDX81456301/2023|EPI_ISL_17856780|2023-06-09
Costa Rica/INC-11487-796517/2023|EPI_ISL_17953750|2023-06-10
Costa Rica/INC-11526-797304/2023|EPI_ISL_17953789|2023-06-08
Costa Rica/INC-11498-796699/2023|EPI_ISL_17953796|2023-06-09
Costa Rica/INC-11528-797306/2023|EPI_ISL_17953784|2023-06-09

[FedeGueli]

I dont think #305 is related with this misplacement. I have already pointed to @angiehinrinchs that there is a B tree of XBB.1.5 misplaced by usher to XBB.1

[NkRMnZr]

I dont think #305 is related with this misplacement. I have already pointed to @angiehinrinchs that there is a B tree of XBB.1.5 misplaced by usher to XBB.1

There's another one #288 with C15024T/T15024C flip-flop

[NkRMnZr]

Updates:

Branch 1

now using query: T10204C,C27005T, C22995G,-T18732C, still fail to catch 5 South African seqs

23-07-20: 1 sequence from California

EPI_ISL_17997578

Branch 2

now using query: C22995G, A29147G, T29515A

23-07-08: 1 seq from Hawaii

EPI_ISL_17961099

23-07-13: 2 seqs from USA

1 from Florida: EPI_ISL_17979207
1 from Alaska: EPI_ISL_17981706

23-07-18: 7 seqs from 3 countries

https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_399bb_65af10.json?f_userOrOld=uploaded%20sample

2 from California, USA: EPI_ISL_17985447, EPI_ISL_17985504, with travel history to El Salvador
1 from Florida, USA: EPI_ISL_17986287
1 from Shanghai, China: EPI_ISL_17994414
3 from Costa Rica: EPI_ISL_17989878, EPI_ISL_17990028

23-07-20: 3 seqs from USA

EPI_ISL_17998483, EPI_ISL_17998499, EPI_ISL_18005324

[FedeGueli]

Branch 2 designated HR.1 via cov-lineages/pango-designation@4257140

[FedeGueli]

Please keep the other monitored if it grows please ping me.

[NkRMnZr]

Please keep the other monitored if it grows please ping me.

I've got another theory, branch 1 could be XBB.1.5 [T17124C > T23018C > T10204C] > C22995G(S:T478R) that got misplaced. There's S:T478R right under T17124C polytomy which is assigned as XBB.1.5.28, this one could be S:T478R right under T17124C > T10204C branch, or simply having dropouts somewhere.

It is really hard to catch T17124C > T10204C > C22995G since all these three mutations are very homoplastic, however if using query: T17124C, T10204C, C22995G, T23602C to catch the largest sub-branch right after C22995G, there will be 46 sequences, plus 10-15-ish missed by this query:
https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice50_genome_a0dd_ffc520.json?c=gt-nuc_23602

do you think this worth a designation/proposal?

[FedeGueli]

thx @NkRMnZr samples are quite old i would keep it unproposed if nothing will change.

[NkRMnZr]

Here's what Branch 1 look like after recent batch from South Africa
https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice2_genome_1b23a_59e0e0.json?c=gt-S_478&label=id:node_7079334

[FedeGueli]

Please rearrange the proposal on Branch 1

[NkRMnZr]

Please rearrange the proposal on Branch 1

Problem is, it's almost impossible to catch them by query, quite a tricky one.

[FedeGueli]

and what about proposing the two main branches of branch 1 as two distinct lineages.??

[FedeGueli]

i think we can close this one.