XCE: Big FY.1 / BQ.1 recombinant hidden in the FY.1 tree (41 samples)

[FedeGueli]

cc @corneliusroemer

Spotted a clear recombinant where a BQ.1* gave its start of Orf1a to FY.1:

https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice2_genome_8b54_8585b0.json?c=gt-nuc_2954&label=id:node_6723854

BQ.1 gave T2954C,C1931A (Orf1a:Q556K), and FY.1 got Orf1a:K47R reverted to K.

Gisaid query:
G18811A, T2954C,C1931A, C15810T

Samples : 34 (but 38 shown on Usher)

EPI_ISL_17008219, EPI_ISL_17092881, EPI_ISL_17189521,
EPI_ISL_17212326, EPI_ISL_17232282, EPI_ISL_17285867,
EPI_ISL_17286110, EPI_ISL_17324727, EPI_ISL_17327420,
EPI_ISL_17397923, EPI_ISL_17421859, EPI_ISL_17440426,
EPI_ISL_17497844, EPI_ISL_17514351, EPI_ISL_17524403,
EPI_ISL_17564884-17564885, EPI_ISL_17615330, EPI_ISL_17655131,
EPI_ISL_17655281, EPI_ISL_17657543, EPI_ISL_17673611-17673612,
EPI_ISL_17677943, EPI_ISL_17696530, EPI_ISL_17696537,
EPI_ISL_17700078, EPI_ISL_17701199, EPI_ISL_17710678,
EPI_ISL_17710680, EPI_ISL_17710723, EPI_ISL_17710729,
EPI_ISL_17710743, EPI_ISL_17719251

[FedeGueli]

I will propose this when it reaches 50

[corneliusroemer]

I just came across this myself, also concluded it was likely a recombinant. Will designate, thanks for the analysis!

[FedeGueli]

THX Cornelius!

[FedeGueli]

XCE