XDF : EG.5.1.3/XBB recombinant(57 seqs, 9 countries)

[xz-keg]

There seems to be a large branch of EG.5.1.3/XBB recombinant.

EG.5.1+C335T,T2334C(rev),C22570T,G27666T

Orf1a:R24C,V690A(rev) Orf7a:E91D

XBB--EG.5.1.3 Breakpoint after 2335, depend on donor.

C335T appears in a lot of XBB* branches.

T2334C(rev),C22570T from EG.5.1.3 G27666T from an EG.5.1.3 branch

Compared with EG.5.1 we have 1 reversion but compared with EG.5.1.3 we have 2 reversions(1889, 2334) so shall be recomb.

GISAID query: C335T,T22930A,G27666T No. of seqs: 55(Canary Islands 1 UK 5 France 2 Germany 1 Ireland 1 Netherlands 1 New Zealand 1 USA 2 Canada 41)

First: EPI_ISL_18309042, USA, 2023-8-29 Latest: EPI_ISL_18504183, Canada, 2023-11-6

usher

usher for EG.5.1.3-donor

[FedeGueli]

It is doubling quite fastly , it is likely boosted by canadian outbreaks and sequencing but still better out it on closer monitoring. I would be surprised if R542C A690V turn out to be detrimental

[xz-keg]

This is the donor of #944 @corneliusroemer

[corneliusroemer]

What's the evidence for recombination here? A single reversion?

[xz-keg]

What's the evidence for recombination here? A single reversion?

Two reversions, as EG.5.1.3 also has 1889 mutated and this one not. So it shall be 1889 and 2334 reversion.

[corneliusroemer]

Hmm, no, 1889 absence isn't additional evidence for recombination, just G27666T is.

No recombination requires:

• reversion of T2334C
• mutation of C335T,C22570T,G27666T

Recombination of XBB with C335T and EG.5.1.3 branch with G27666T explains a) the reversion and b) the extra mutations

So there's a total saving of 4 mutations. I wonder how many such relatively-weak-evidence maybe-recombinants there are.

Most likely 5' donor is EG.10.1, as it represents 60% of recent XBB + 335T + not T2334C

[xz-keg]

Hmm, no, 1889 absence isn't additional evidence for recombination, just G27666T is.

No recombination requires:

• reversion of T2334C
• mutation of C335T,C22570T,G27666T

Or reversion of C1889T, T2334C and mutation of C335T on the EG.5.1.3+Orf7a:E91D branch.
So 2 rev+1 mut or 1 rev+3 mut.

[FedeGueli]

Designated XDF via https://github.com/cov-lineages/pango-designation/commit/f9269e87590d0afe646aeee7479171a797244e4c