XDW: JN.2/XDA recombinant with additional S:R346T(8 seqs, Japan)

[xz-keg]

One singlet in #991 gets company.

JN.2--XDA

Breakpoint between 23424 and 23603(between S:622 and S:680)

Additional mutations: T1030C, C21301T,G22599C
S:R346T
Orf1b:P2612S

T1030C, C21301T from a JN.2 branch.
G22599C is private mutation.

GISAID query: C28471T,A2127G,T1030C
No. of seqs: 2(Japan)

EPI_ISL_18854347, 2024-1-16
EPI_ISL_19005974, 2024-1-31

usher

[xz-keg]

@FedeGueli It is a mixed spike, 0 to 621 is BA.2.86+S:R346T, 622 to end is XDA.

[FedeGueli]

@FedeGueli It is a mixed spike, 0 to 621 is BA.2.86+S:R346T, 622 to end is XDA.

Ah sorry i added for mistake it is not even a JN.1

[corneliusroemer]

It's now 7 sequences - quite an interesting recombinant as it's effectively like XDQ + S:R346T, S:P681H, S:A701V (and a branch with S:A263V)

These are all quite possibly fitness increasing compared to XDQ which is doing ok even without the extra 475V of XDQ.1

[corneliusroemer]

Just rediscovered this on the Usher tree - designated XDW as it's clearly circulating and has an interesting genotype.

How are you certain that XDA is the donor rather than XDA's donor HN.5? Does it share a mutation with XDA only @aviczhl2? In general it's easier to remember the genotype if one refers to the non-recombinant donor (if possible) as recombinants are hard to remember!

[xz-keg]

Just rediscovered this on the Usher tree - designated XDW as it's clearly circulating and has an interesting genotype.

How are you certain that XDA is the donor rather than XDA's donor HN.5? Does it share a mutation with XDA only @aviczhl2? In general it's easier to remember the genotype if one refers to the non-recombinant donor (if possible) as recombinants are hard to remember!

XDA is more widespread than its specific HN.5 donor I guess?