Closed NkRMnZr closed 1 year ago
@NkRMnZr there is an error, this lineage DO HAVE M:D3N :
I looked at the putatitve donors, but first to clarify the proposal: This is XBB.+486P until maximum E:10 ( 26272) and then from 26272 to end is BQ*
I think i have identified the BQ.1 side parent : looking at Bq.1 from 2023 carrying both Orf8:V62L and N:P365L i found just two sequences from Indonesia belonging to BQ.1.1.25 (EPI_ISL_17683939
EPI_ISL_17683936) As shown below they have no difference in the recombinant side to the lineage proposed here:
https://cov-spectrum.org/explore/World/AllSamples/Past6M/variants?aaMutations=S%3AT478I%2CS%3A214H&aaMutations1=Orf8%3AG8*&nextcladePangoLineage1=XBB.1*&nucMutations2=C28312T%2CC28657T%2CG28681T%2CC29367T&nextcladePangoLineage2=BQ.1.1.25*&analysisMode=CompareEquals&
While for the xbb.1 side i didnt find any certain parent: ORF1b:T1621I doesnt seem circualting in Indonesia while io found some XBB.1.9.1 with that in Australia that frequently collects lineages from Indonesia (EPI_ISL_17561522) but too weak as proof of anything
@NkRMnZr there is an error, this lineage DO HAVE M:D3N :
Thanks @FedeGueli , just realized I used the earlist sequence for analysis and it happens to be the only one without M:D3N. Metadata shows the sequence are from different patients so either dropouts or these seqs are from different recombinantion events, giving there's a 2 months gap between 1st and 2nd sequences.
Could the XBB.donor be XBB.1.5.40? At top of my head that's the only XBB. with T478I ....That's quite rare as a 478 mutation. But I understand XBB.1.5.40 has never been sequenced in Indonesia, Australia or South Korea : only USA.
Could the XBB.donor be XBB.1.5.40? At top of my head that's the only XBB. with T478I ....That's quite rare as a 478 mutation. But I understand XBB.1.5.40 has never been sequenced in Indonesia, Australia or South Korea : only USA.
I'm afraid not, for it doesn't have T17124C, but yeah 478I is a bit rare by that time sequenced for the first time.
XCD
Transferred from sars-cov-2-variants/lineage-proposals#148
Query: G22203A, C22995T, C28657T Earliest seq: 2023-01-26 (EPI_ISL_17683933, Indonesia) Latest seq: 2023-05-25 (EPI_ISL_17742133, Australia) Sampled in Countries: Indonesia (6), South Korea (5), Australia (1, NSW), USA (1, Virginia)
Genomes: EPI_ISL_17647594, EPI_ISL_17647595, EPI_ISL_17647596, EPI_ISL_17723340, EPI_ISL_17723346, EPI_ISL_17742133, EPI_ISL_17716667, EPI_ISL_17736554, EPI_ISL_17736565, EPI_ISL_17683903, EPI_ISL_17683933, EPI_ISL_17736545, EPI_ISL_17736560
UShER: https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice2_genome_3dd43_ed0b40.json?f_userOrOld=uploaded%20sample![Detailed](https://github.com/sars-cov-2-variants/lineage-proposals/assets/125747944/0192eec5-9cac-4634-a1b6-2d78b7f7d1d8)
Evidence:![Mut](https://github.com/cov-lineages/pango-designation/assets/125747944/0e852157-ef0a-4a80-80aa-5b7a29a82378)
it does not have BA.5's G26529A (M:D3N), either a second breakpoint or simply reversionEdit: the only sequence that witoutht G26529A (M:D3N) is the earlist sequence EPI_ISL_17683933, others should all have it. Thanks to @FedeGueli for correction.Conclusions & Putative Donors: (cc. @FedeGueli see comments for details)
Private mutations: C12357T (ORF1a:T4031I), T18006C (ORF1b:L590L), A19173G (ORF1b:T1902T), G22203A (S:R214H), C22995T(S:T478I), G28077T (ORF8:V62L), C28657T (N:D128D)