XBB.1 + S:486P + S:456L with G4006A, T17067C, T26012G (26 seqs 2022-06-03) circulating in Reunion, Canada, Ireland , Spain)

[corneliusroemer]

There are around 10 sequences of XBB.1 + S:486P + S:456L that have extra nuc mutations G4006A, T17067C, T26012G (ORF3a:F207C)

What confuses me is that 26012G is also part of FE.1, which also has the same Spike XBB.1 + S:486P + S:456L

This could be chance, or it could be recombination or the origin of FE.1 is different than I thought (A8001G didn't happen first)

https://cov-spectrum.org/explore/World/AllSamples/Past6M/variants?variantQuery=nextcladePangoLineage%3AXBB.1*+%26+S%3A486P+%26+%5B3-of%3AC1878T%2C%09G4006A%09%2CT17067C%2C%09T20600C%2C%09T22928C%2C%09T26012G%2C%09C27881T%09%2CG29449T%5D&nextcladePangoLineage1=FE.1*&nextcladePangoLineage2=XBB.1.5*&analysisMode=CompareEquals&

Some recent sequences:
hCoV-19/USA/MS-CDC-VSX-A079750/2023|EPI_ISL_17618604|2023-04-15
hCoV-19/USA/CA-CDC-LC1038686/2023|EPI_ISL_17619098|2023-04-19
hCoV-19/USA/PA-CDC-LC1038837/2023|EPI_ISL_17619168|2023-04-20

Usher puts them in a weird (probably wrong) place with lots of reversions:

https://next.nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_131c1_688ca0.json?f_userOrOld=uploaded%20sample

Gisaid query: G4006A, T17067C, T26012 (edited)

[FedeGueli]

12 as today last one from TN, Usa

[FedeGueli]

14 as today with your query @corneliusroemer G4006A, T17067C, T26012G but Usher shows me 15 all in the branch that has all the three nuc mutation of Orf7b:A43L (C27881T, G27882C, C27883T reverted so Orf7b:43A likely just a misbranching of this one or artefact? cc @ryhisner @AngieHinrichs

https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_22104_362660.json?c=gt-nuc_27882&label=id:node_674574

[ryhisner]

The ORF7b:A43L thing is definitely real—it's repeatedly shown up in a variety of sequences from all over the world throughout the course of the pandemic—though the branches that have it reverted almost certainly don't belong in this tree. It's a TRS thing—those three nuc mutations provide extended homology for the ORF8 TRS, which should enhance its expression. It's very strange to see this happening in lineages with ORF8:G8*, but I guess it goes to show that there's more going on under the surface than we often realize. My guess is that increasing the expression of the 7-AA ORF8 peptide in XBB.1 ensures more nucleotides tRNAs & other cell resources are preserved for N and ORF9b, but I could be completely wrong.

[FedeGueli]

Thx @ryhisner great explanation!

[FedeGueli]

Scratch this one the three Canadian are unrelated to this one: https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_2f9e9_9ff7e0.json?label=id:node_8616292

18 seqs as today last three coming fom Canada found with G4006A, T17067C, T26012

[FedeGueli]

last tree: https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_1c3ff_c9a290.json?label=id:node_6903416

[FedeGueli]

23 seqs as today

[corneliusroemer]

Just rediscovered this, sequences from French Guiana (right next to Brazil) make this look quite strongly like an FE.1 recombinant, so I've designated it as XCF

[FedeGueli]

Thx @corneliusroemer Guyana Suriname and french Guyana seems under a surge (Cases and deaths for Suriname, Cases for Guyana, still not much for French Guyana) and they are next to the Brazilian region of AMAPA' from some worrying warning has been raised. So very good to designate everything we are certainly circulating there.

source: https://www.who.int/publications/m/item/weekly-epidemiological-update-on-covid-19---8-june-2023

[FedeGueli]

PS : i agree it is a recombinant it took the orf1ab from some other XBB lineage:

https://cov-spectrum.org/explore/World/AllSamples/from%3D2023-03-31%26to%3D2023-06-10/variants?nucMutations=G4006A%2CT17067C%2CT26012&nextcladePangoLineage1=FE.1*&analysisMode=CompareEquals&

[FedeGueli]

XCF