XCD: Possible XBB.1.5* × BQ.1* recombinant with ORF1a:T4031I, S:R214H, S:T478I, ORF8:V62L (13 seqs, 4 countries)

[NkRMnZr]

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

Evidence:

• Somehow nextclade recognize it as XBW, but it is not, for it doesn't have T22612C, C24130T, G29260A
• it does not have many of XBB.1.5's T17124C
• it has XBB.1's G22317T (S:G252V) instead of XBB.2.3's A22320G (S:D253G), ruled out possiblity of XBB.2.3* + S:T478I
• it has S:F486P (T23018C, T23019C), one of the donor could be either XBB.1.5 pre T17124C or other XBB.1 + S:F486P
• it does not have XBB's C25416T, A26275G (E:T11A), means breakpoint before C25416T, probably the reason being recognized as XBW
• it does not have BA.5's G26529A (M:D3N), either a second breakpoint or simply reversion Edit: 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.
• it does not have XBB's M:D61L (G27382C, A27383T, T27384C)
• it has BQ.1's ORF9b:P10F (C28311T, C28312T), interestingly XBB.1.5.57 (donor of XBL, without T17124C) also has it
• it has BQ.1's G28681T (N:E136D)

Conclusions & Putative Donors: (cc. @FedeGueli see comments for details)

• 5' end donor could be a pre T17124C XBB.1.5*, or any other XBB.1* that has S:F486P
• breakpoint between 23019 and 25416.
• 3' end donor could be BQ.1.1.25

Private mutations:
C12357T (ORF1a:T4031I), T18006C (ORF1b:L590L), A19173G (ORF1b:T1902T), G22203A (S:R214H), C22995T(S:T478I), G28077T (ORF8:V62L), C28657T (N:D128D)

[FedeGueli]

@NkRMnZr there is an error, this lineage DO HAVE M:D3N :

[FedeGueli]

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]

@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.

[focosi-cyber]

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.

[NkRMnZr]

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.

[JosetteSchoenma]

XCD