Closed NkRMnZr closed 1 year ago
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
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
Updates:
now using query: T10204C,C27005T, C22995G,-T18732C, still fail to catch 5 South African seqs
now using query: C22995G, A29147G, T29515A
Branch 2 designated HR.1 via https://github.com/cov-lineages/pango-designation/commit/425714014f29d5f4288d9f3783debe09728d15ed
Please keep the other monitored if it grows please ping me.
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?
thx @NkRMnZr samples are quite old i would keep it unproposed if nothing will change.
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
Please rearrange the proposal on Branch 1
Please rearrange the proposal on Branch 1
Problem is, it's almost impossible to catch them by query, quite a tricky one.
and what about proposing the two main branches of branch 1 as two distinct lineages.??
i think we can close this one.
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 ![insertion](https://github.com/sars-cov-2-variants/lineage-proposals/assets/125747944/fb78d808-2212-4cb5-83e8-fb2804917849)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 ![branch2qc](https://github.com/sars-cov-2-variants/lineage-proposals/assets/125747944/be8aca37-3f6b-4253-87b5-f1b68a9e119d)