Potential Delta/Omicron Recombinant Lineage with Likely Breakpoint at NSP3 (30 Seqeuences in the UK as of 2022/02/17)

[c19850727]

Description
Recombinant between: AY.4 (or one of AY.4 sublineages) & BA.1
Earliest sequence: 2022/01/07 (UK-England)
Most recent sequence: 2022/2/10 (UK-England)
Countries circulating: UK-England (30 sequences)

Likely breakpoint: between 5387 and 6511 (NSP3), which is interestingly quite different from other potential Delta/Omicron recombinant lineages.

Conserved Nuc mutations and AA changes (those in red frames are likely from the donor from the AY.4 side):

Evidence
Nextclade downsampled tree (unrooted):

Nextclade downsampled tree (starting from 21M):

Usher tree:

https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_21f61_a9120.json?c=gt-ORF1ab_664&label=nuc%20mutations:G5386T

Genomes:
EPI_ISL_8894978, 8899193, 8964736, 9024950, 9027096, 9074902, 9174471, 9247732, 9254198, 9256573, 9284798, 9296126, 9310093, 9399416, 9411495, 9589270, 9641789, 9681404, 9727711, 9729847, 9732451, 9783055, 9790074, 9813122, 9818970, 9825890, 9827103, 9827194, 9866660, 9996515

[c19850727]

4 more sequences: EPI_ISL_10106252, 10348464, 10357090, 10388349.

[chrisruis]

Thanks @c19850727 We've added this as lineage XF in v1.2.133