XDM: XDA, GW.5.1.1 (or GW.5.3.1), XDA sandwich recombinant (14 seqs, UK)

[NkRMnZr]

Query: T24046C, C27059T or T8908C, A13693G, C22986T
Earliest seq: 2023-12-02 (EPI_ISL_18598919, England)
Latest seq: 2023-12-02 (EPI_ISL_18598920, England)
Sampled Countries: UK (2: EN)

Recombinant Profiles:

• Placement on Phylogenetic Tree: XDA > C27059T > G22927T(S:L455F, C22986T(S:A475V), C22995T(S:T478I, T>K>R>I), rev_T23664C(S:rev_V701A), C24034T(S:N824N), T24046C(S:L828L), G25599T(ORF3a:W69C)
• Donor A: XDA, upstream from 5' end to 1st breakpoint, downstream from 2nd bp to 3' end.
• Donor B: GW.5.1.1 or GW.5.3.1, between 2 bps
• 1st Breakpoint: Between nuc_22107/spike_182 to nuc_22926/spike_455 if one of the donor is GW.5.1.1; Between nuc_22113/spike_184 to nuc_22926/spike_455 if one of the donor is GW.5.3.1
• 2nd Breakpoint: Between nuc_24047/spike_829 to nuc_25838/ORF3a_149
• Private mutation(s): ORF3a:W69C (G25599T)
• Effectifly this would be XDA with FLip combo plus A475V and T478I at a cost of A701V, OR GW.5.1.1 with its ORF7ab restored plus K182Q and ORF9b:I5T
• Details of mutations:
  

Genomes:

England/CLIMB-CM7Y89IF/2023|EPI_ISL_18598919|2023
England/CLIMB-CM7YFFCT/2023|EPI_ISL_18598920|2023

UShER:
https://nextstrain.org/fetch/genome-test.gi.ucsc.edu/trash/ct/subtreeAuspice17_genome_test_23e00_3e3230.json?f_userOrOld=uploaded%20sample&label=id:node_3348095

[FedeGueli]

Great catch and great deal on the paper : fast XDA got FLip 475V 478 and 554 in one shot

[xz-keg]

Breakpoint shall be after S:182 if the donor is GW.5.1.1

[xz-keg]

6 now

[NkRMnZr]

Tracking updates

12-26, 5 seqs from UK EPI_ISL_18688239, EPI_ISL_18688415-18688416, EPI_ISL_18688421, EPI_ISL_18688850
01-02, 4 seqs from UK EPI_ISL_18694524, EPI_ISL_18707906, EPI_ISL_18708024, EPI_ISL_18708035
01-08, 3 seqs from UK

[FedeGueli]

8 now (+1 England)

[FedeGueli]

11 now, growing fast.

[NkRMnZr]

01-08, 3 seqs from UK EPI_ISL_18727091, EPI_ISL_18727726, EPI_ISL_18727734

[corneliusroemer]

It's an interesting one, are we sure that XDA is a parent or could a parent of XDA be a parent here? I guess XDA as parent is not too unlikely given that XDA is quite prevalent in the middle east and Indonesia (Muslim majority countries) and so is GW.5).

It has a potentially quite competitive genotype

https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_1a9f3_ead600.json?c=country&label=id:node_3303661

Two new sequences uploaded from England (2023-12-28) Jan 09, so it's 16 now. I think I'll designate.