Potential BA.2.12.1 and BA.4 recombinant with multiple breakpoints (38 seqs as of 2022-07-18, mainly UK)

[c19850727]

Description

Recombinant between: BA.2.12.1 and BA.4
Earliest sequence: 2022/06/09 (UK-England)
Most recent sequence: 2022/07/01 (UK-England)
Countries circulating: UK-England (17/19)
Cases found at border entry: Korea ex-Maldives (2/19)
Likely breakpoint: to be updated later
Mutations from potential BA.2.12.1 donor: ORF1a:L3201F, S:S704L, A12160G, C15009T
Mutations from potential BA.4 donor: S:69/70del, S:L452R, S:F486V, S:R493Q reversion, S:N658S

GISAID query: Spike_H69del, Spike_L452R, Spike_S704L, Spike_N658S, NSP4_L438F
Cov-spectrum query: T15009C, 9866T, 23673T, 23535G, 22917G, 23040A

Evidence

Usher tree:

https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_150a2_6de290.json?branchLabel=Spike%20mutations&c=gt-nuc_23040,15009&label=nuc%20mutations:T22917A

Genomes:

EPI_ISL_13338123, EPI_ISL_13515716, EPI_ISL_13518141, EPI_ISL_13603584, EPI_ISL_13690214-13690215, EPI_ISL_13693012, EPI_ISL_13693033, EPI_ISL_13693042, EPI_ISL_13693048, EPI_ISL_13693102, EPI_ISL_13693105, EPI_ISL_13693115, EPI_ISL_13693124, EPI_ISL_13693127, EPI_ISL_13693130, EPI_ISL_13693132, EPI_ISL_13693157-13693158

[agamedilab]

Most UK sequences originate from the sameupload (7.7.2022), sample day (30.6.22) and sequencing lab (Welcome Sanger) so they possibly originate from the same sequencing run.

Some of them carry some non-ACGTN characters which is a bit suspicous.

[c19850727]

Thanks @agamedilab I didn't notice this.

I've been monitoring this cluster before this big upload from Welcome Sanger, and what prompted me to propose was those 2 mysterious Korean sequences with recent travel history from Maldives.

It might imply some undetected transmission either among tourists in one of the Maldivian islands, or, in a worse scenario, at one of Middle Aast flight transit hubs.

[c19850727]

20 sequences as of 2022-07-08.

[c19850727]

23 sequences as of 2022-07-08, and now from a different lab in the UK (PHE).

[c19850727]

24 sequences as of 2022-07-09. Newly found in US-WA.

[c19850727]

26 sequences as of 2022-07-09. Newly found in Israel.

[c19850727]

30 sequences as of 2022-07-11.

[thomasppeacock]

UKHSA have been having a look at this and as far as they can see it looks legitmate (no evidence of mixed bases at BA.2/BA.4 lineage defining sites).

@chrisruis although this hasnt yet hit the threshold for minimum number of recombinants I reckon it might be worth assigning as i) this is 30 sequences in the UK's current much lower sequence numbers, ii) its an interesting/unique recombinant (2 breakpoints ~Spike region) and iii) clear evidence of international spread. Thanks!

[InfrPopGen]

Thanks for submitting. We've added recombinant lineage XAJ with 35 newly designated sequences, and 0 updated designations. Defining mutations (clade root): A23535G, A27259C