Potential BA.2.76/BA.5.2 recombinant with spike changes from both donors (50 seqs as of 2022-11-12)

[c19850727]

I am proposing this potential recombinant with only 5 sequences based on its mutation profile at spike protein.

It acquires through the recombination event S:Y248N and S:R346T from BA.2.76 to a BA.5.2 backbone, which are both amino changes associated with relative growth advantages among multiple other Omicron sublineages.

It also has a private NSP5 change (ORF1a:T3284I)

Description

Recombinant between: BA.2.76 and BA.5.2
Earliest sequence: 2022/07/05 (UK-Scotland)
Most recent sequence: 2022/07/13 (UK-Wales)
Countries circulating: UK (4 in Scotland and 1 in Wales)
Likely breakpoint: between 22601 and 22915 (Spike S1)
Mutations on branch: C10116T (ORF1a:T3284I), C11665T, A19812G, T22304A (S:Y248N), G22599C (S:R346T), A24676G, T26180C (ORF3a:I263T)

Nuc mutations (those in red frames are likely from BA.2.76):

GISAID query: NSP5_T21I, Spike_Y248N, Spike_R346T, Spike_F486V, M_D3N
Alternative GISAID query (for sensitivity purposes): Spike_Y248, Spike_R346T, Spike_F486V, Spike_L452R, NS3_I263T
cov-spectrum query: C10116T, C11665T, A19812G, T22304A, T26180C

Evidence

Usher tree:

https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_2abd6_75b790.json?branchLabel=aa%20mutations&c=gt-nuc_10116&label=nuc%20mutations:C9866T

Genomes:

Only 2 of these 5 genomes are in GISAID with an accession number as of 2022-07-31.
hCoV-19/Scotland/LSPA-3EC6F3F/2022
hCoV-19/Scotland/LSPA-3EC6F3F/2022 | EPI_ISL_14043424
hCoV-19/Scotland/SCOT-16494/2022 | EPI_ISL_13769003
hCoV-19/Wales/PHWC-PKBQOM/2022
hCoV-19/Scotland/LSPA-3EBC8D7/2022

[c19850727]

There's an unrelated but similar recombinant (between BA.2.76 and BF.3) that has been placed next to #896 by Usher, probably because of identical breakpoint.

[c19850727]

A quick update: There are 15 sequences now, with the latest one collected on 2022-09-17.
There is also a distinct sub-branch with an additional N:A152V found in US-CA (3 genomes).

[c19850727]

This recombinant started to grow again after a hiatus of almost one month.
Now there are 33 sequences as of 2022-11-01.

5 new sequences have just been uploaded from UK-England with a very recent collection date.

https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_22ef4_12edd0.json?c=gt-nuc_11665&label=nuc%20mutations:C10116T,C11665T,A19812G,T22304A,G22599C,A24676G,T26180C

[c19850727]

12 new sequences since last update (on 2022-11-01), and 45 sequences in total.
Also newly found in Slovakia, Germany and Switzerland.

[c19850727]

5 new sequences as of 2022-11-12, all very recently collected.
50 in total now.
Newly found in Italy.

Also GISAID query is updated: Spike_Y248, Spike_R346T, Spike_F486V, Spike_L452R, NS3_I263T

[InfrPopGen]

Thanks for submitting. We've added recombinant lineage XBG with 14 newly designated sequences, and 0 updated designations. Defining mutations C10116T (ORF1a:T3284I), T22304A (S:Y248N), G22599C (S:R346T), T26180C (ORF3a:I263T), A24676G, A19812G, C11665T.

[JosetteSchoenma]

XBG