Another EG.5.1/DV.7.1 recombinant that may be removed by usher(27 seqs, 4 countries)

[xz-keg]

There is another EG.5.1/DV.7.1 recombinant different from XCT.

EG.5.1--DV.7.1 Breakpoint between 14125 and 15025.

Additional mutations: del518_520, C1471T, C3397T, T14124A,C15924T, C29518T,T29793A

Orf1a: M85-

del518_520, C1471T,T14124A from a EG.5.1 branch having S:F186L C15924T, C29518T, T29793A from a DV.7.1 branch

C3397T are private.

GISAID query:C3397T,T14124A,C15924T(edited) No. of seqs: 4(Belgium 1 Canada 3)

EPI_ISL_18393248, Belgium, 2023-9-27 EPI_ISL_18395603,18395605-18395606, Canada, 2023-10-10

@AngieHinrichs, please add them to usher tree.

usher

The top branch is XCT, the proposed is lower branch.

usher for EG.5.1 donor

usher for DV.7.1 donor

[FedeGueli]

+1 Belgium

[xz-keg]

EPI_ISL_18406446 @AngieHinrichs

[xz-keg]

+1 Switzerland without 12599, edit query.

[FedeGueli]

+1 Switzerland without 12599, edit query.

thank you

[FedeGueli]

+3 Canada

please propose once it reaches 25

[xz-keg]

+3 Canada

please propose once it reaches 25

Shall be +5, 2 of the seqs has 518 masked. altered query.

[FedeGueli]

Thx for the new query

[ryhisner]

Interesting that this one has T29793A. This is directly adjacent to the octanucleotide motif (ONM), whose purpose is unknown but which I believe is absolutely conserved in either all beta-coronaviruses or all coronaviruses. T29793A has only been in ~2200 sequences ever according to CovSpectrum, and I'd bet that a fair fraction of those are sequencing artifacts, which are pretty common in the 3' UTR.

True to form, the ONM is virtually never mutated in SARS-CoV-2 genomes. It would be interesting to try to find which mutations in the ONM are real, if any, but it's a Herculean task to try to sort out real 3' UTR mutations from artifactual ones. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7766253/

[xz-keg]

+1 Italy