search

sars-cov-2-variants / lineage-proposals

Repository to propose and discuss lineages
43 stars 2 forks source link

Multiple JN.1* lineages with S:F32del #1768

Closed aviczhl2 closed 1 month ago

aviczhl2 commented 2 months ago

It seems that like S:S31del, there is also lots of S:F32del branches emerging.

As it is basically having similar function as S:S31del, DeFLiRT/DeFLuQE still works. 

### Tasks
- [x] **DeFLiRT Branch 1, designated KP.2.6** Query:  del21656,T21752A
- [ ] **DeFLiRT Branch 2**, KP.2+T22795G+T24637G+S:F32del, Proposed in https://github.com/cov-lineages/pango-designation/issues/2715
- [x] **DeFLiRT Branch 3,DEAD**, KP.2+T22795G+Orf1a:A1485V, Orf1b:T1363I, S:H445Y, S:F32del, Query: del21656_21658, G22895T,C17555T, 9 seqs, USA, UK, France, Netherlands (likely dead)
- [ ] **DeFLiRT Branch 4**, KP.2+Orf1a:P1803L, S:K558N, S:F32del, Proposed in https://github.com/cov-lineages/pango-designation/issues/2736
- [ ] Branch 5,, JN.1+Orf1a:A339V,S:F32del, Query: del21656_21658, T25818C, 11 seqs, Ukraine, many with S:R346T
FedeGueli commented 2 months ago

Credit to @Sinickle that spotted it in KP.2.6

FedeGueli commented 2 months ago

Most of the samples are very recent soemthing to watch thks @aviczhl2 for opening this one.

Mydtlwn commented 2 months ago

To distinguish from S:S31del, I suggest adjusting the combined name of S:F32del to De2FLiRT or De2FLuQE. If both mutations are present, they can be called 2DeFLiRT and 2DeFLuQE. Those with S:F59L can also be referred to as 2FLiRT and 2FLuQE.

aviczhl2 commented 2 months ago

To distinguish from S:S31del, I suggest adjusting the combined name of S:F32del to De2FLiRT or De2FLuQE. If both mutations are present, they can be called 2DeFLiRT and 2DeFLuQE. Those with S:F59L can also be referred to as 2FLiRT and 2FLuQE.

It is unlikely for both to present simutaneously, as it will destroy the N Glycan and may not grow.

Mydtlwn commented 2 months ago

You're absolutely right, but this is just one possible scenario. Actually, I don't favor the simultaneous occurrence of both mutations either.

rchorowski commented 2 months ago

When did you add the tag "N Glycan" to the repo? I mean when did you start to tag the lineages with this tag?

aviczhl2 commented 1 month ago

Branch 2 becomes 21, branch 4 becomes 17

FedeGueli commented 1 month ago

Branch 2 becomes 21, branch 4 becomes 17

Br.2 is 30% of recent samples collected (or related to) Ecuador. Please propose it , thx for tracking it.

FedeGueli commented 1 month ago

When did you add the tag "N Glycan" to the repo? I mean when did you start to tag the lineages with this tag?

since it became relevant with DeFLIRT after DEFLiRT

aviczhl2 commented 1 month ago

Branch 4 becomes 24. The other 2 seems dead.

aviczhl2 commented 1 month ago

Branch 5 becomes 10 and still circulating in Ukraine in July.

aviczhl2 commented 1 month ago

And Branch 4 is 26 in 11 countries now.

FedeGueli commented 1 month ago

And Branch 4 is 26 in 11 countries now.

Please propose it on Pango

aviczhl2 commented 1 month ago

All significant branches are proposed. Close this one.