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XCK: FL.1.5.1 x BQ.1.2.2 Recombinant, 6 seqs, Nigeria and US-TX #630

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c19850727 opened this issue Aug 17, 2023 · 4 comments
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XCK: FL.1.5.1 x BQ.1.2.2 Recombinant, 6 seqs, Nigeria and US-TX #630

c19850727 opened this issue Aug 17, 2023 · 4 comments
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designated Emerged in an undersampled area Actual infection toll may be much larger than number of sequences suggest recombinant S:456 S:478 Truncated Orf(3-10) XCK

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@c19850727
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c19850727 commented Aug 17, 2023 •
edited by FedeGueli
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image

https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_3f3b7_e4b1b0.json?c=gt-ORF8_90&label=id:node_6930474

Query: G3242A, C28163A
Earliest sequence: EPI_ISL_18110467, 2023-07-20, Nigeria
Most recent sequence: EPI_ISL_18098706, 2023-08-04, US-TX

Breakpoint is likely somewhere between nuc 23665 (spike 701) and 25415 (ORF3a 8). Everything upstream is from a FL.1.5.1 donor, and everything from 25416 to 3' is from BQ.1.2.2 donor.

Unique AA changes from BQ.1.2.2: ORF3:255/258del, ORF8:C90stop

Sequences: EPI_ISL_18098706, EPI_ISL_18110467, EPI_ISL_18110470

EDITED i (F) add a rapid portrait of this recombinant
Schermata 2023-08-23 alle 16 12 39
@FedeGueli
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Great catch Saka it is a FL.1.5 spike (with Orf1b:2557) that got rid of E:11 Orf6:61 putative attenuating mutations and orf8:8* but orf8 expression is severely ablated by 27889 . and also truncated by orf8:90* .

So coming from an undersampled area is something to track closely i think it should be proposed if reaches 10 in the next two weeks.

@FedeGueli FedeGueli added To be proposed Green light for proposal Truncated Orf(3-10) Emerged in an undersampled area Actual infection toll may be much larger than number of sequences suggest labels Aug 17, 2023
@NkRMnZr
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NkRMnZr commented Aug 23, 2023 •
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6 now, the lineage has been pulled to a familiar phylogenetic tree cluster
https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_37f6e_5e2750.json?c=gt-S_456,478,486&label=id:node_7113179
poly

can confirm USA/TX-TAMGHRC-SHS_97708/2023|EPI_ISL_18111443|2023-07-24 have Ns around 416 to 462 of S gene
image

@FedeGueli
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Please propose it @c19850727 .
Thx @NkRMnZr

@FedeGueli FedeGueli changed the title FL.1.5.1 x BQ.1.2.2 Recombinant, 3 seqs, Nigeria and US-TX FL.1.5.1 x BQ.1.2.2 Recombinant, 6 seqs, Nigeria and US-TX Aug 23, 2023
@FedeGueli FedeGueli added S:456 S:478 combo It has a couple of mutation in RBD and removed Rapid review needed labels Aug 23, 2023
@c19850727 c19850727 mentioned this issue Aug 26, 2023
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@FedeGueli FedeGueli added designated and removed To be proposed Green light for proposal combo It has a couple of mutation in RBD labels Aug 31, 2023
@FedeGueli
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designated XCK via cov-lineages/pango-designation@4749974

@FedeGueli FedeGueli added the XCK label Oct 16, 2023
@FedeGueli FedeGueli changed the title FL.1.5.1 x BQ.1.2.2 Recombinant, 6 seqs, Nigeria and US-TX XCK: FL.1.5.1 x BQ.1.2.2 Recombinant, 6 seqs, Nigeria and US-TX Oct 16, 2023
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designated Emerged in an undersampled area Actual infection toll may be much larger than number of sequences suggest recombinant S:456 S:478 Truncated Orf(3-10) XCK
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