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Repository for suggesting new lineages that should be added to the current scheme
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BA.2.86.1/EG.5.1* (or XDT or or XDL or EG.1 or ?) 32 samples 6 countries #2501

Open JosetteSchoenma opened 4 months ago

JosetteSchoenma commented 4 months ago

Description: BA.2.86.1/EG.5.1 (or XDT or XDL or EG.), BA.2.86.1 Spike, EG.5.1 end. Private mutations: Really private: C1779T, C2070T, C8802T From BA.2.86.1: T11614C Breakpoints: between nucleotide 26529 and 27507 if it recombined with an EG.5.1, Since XCT, XDL and EG.1 do not have C26833T which this recombinant and EG.5.1 do have, the breaking point would be between 26833 and 27507, if it recombined with one of these 3. There are a lot of BA.2.86.1 with C26833T. Earliest sequence: 2023-11-03 from the Netherlands Most recent sequence: 2024-01-29 from Germany Countries circulating: The Netherlands 9 , Germany 8, Slovenia 7, the US 2, Denmark, England and Sweden 1. GISAID query: C1779T, A7842G, A27507C

Note: Both XDS and XDS lookalike EPI_ISL_18612396 do not have many mutations differently from nucleotide 11614 onward, but since they are both from a later date, I do not think it recombined with one of them. The other way around is a bit more likely, but after studying their mutations, I do not think so. Hard to be sure though. I added them to my Nextclade overview to show what I mean. EPI_ISL_18612396 has no A22786C in the Spike like XDS and this recombination, but it does have a T22926C (S:L455S), which XDS and all but one of this recombination miss. XDS and the lookalike have A17637G and C29625T extra and XDS has C29409T besides that. image Please note the extra info on XDS and the Swiss lookalike @aviczhl2 provided in this issue as well. https://github.com/sars-cov-2-variants/lineage-proposals/issues/1267

Nextclade: image

Usher: image

Original proposal: https://github.com/sars-cov-2-variants/lineage-proposals/issues/1185

aviczhl2 commented 4 months ago

It shall be XBB.1.9.2 except EG.5 ? EG.1, EG.3, EG.4 and EG.9 are also impossible for their 3' mutations.

JosetteSchoenma commented 4 months ago

It shall be XBB.1.9.2 except EG.5 ? EG.1, EG.3, EG.4 and EG.9 are also impossible for their 3' mutations.

I think EG.5.1* is possible. Many of them do not have C29625T. Maybe because coverage is often bad at the end. All these have a nearby deletion at the end.