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Repository for suggesting new lineages that should be added to the current scheme
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Rapid identification of BA.2.86 branches (=/>2seqs)((Archived) #2236

Closed FedeGueli closed 1 year ago

FedeGueli commented 1 year ago

BA.2.86

Branches (more than 1seq only): 1 = BA.2.86.1 = Orf1a:K1973R (A6183G), C12815T query :A6183G, C12815T 1a : Orf1a:Y621C (A2127G) Query : A6183G, C12815T, A2127G 1a1: G2527A, ORF1a:P971L (C3177T) query:G2527A, C3177T, A2127G 1b : N:E378Q (G29405C) Query : G29405C,A6183G,C12815T 1c S:748Q ( G23804C), C11152T Query: ,A6183G,G23804C, C11152T 1d: Orf1b:T1274I(T11614C), C17288T : query: T11614C, C17288T 1e: C7528T Query: A7842G,C7528T,A6183G 1f: A23566T, N:T135I (C28677T) Query: A23566T ,C28677T,A6183G 1g: C13971T,C29635T Query:C13971T,C29635T,A6183G 1h: ORF1a:K2507R (A7785G),Orf1a:A2784V (C8616T) Query:A7785G, C8616T,A6183G 1i: T11614C Query: T11614C, C12815T,A6183G

2 ORF7a:E22D (G27459T) Query: A7842G,G27459T 2a: C1663T Query : C1663T, G27459T,A7842G

3 C2137T, S:I670V (A23570G), Orf8:T87I (C28153T), N:G243S (G29000A)

4 C1960T Query : C1960T,A7842G,G8393A

5 C9226T, G14347A, Orf1b:D294N (G14347A), C15108T Query : C9226T, G14347A,C15108T

cc @corneliusroemer @AngieHinrichs based on Cornelius Tree: https://nextstrain.org/groups/neherlab/ncov/BA.2.86?c=gt-nuc_25000,25207 Schermata 2023-09-01 alle 10 09 27

corneliusroemer commented 1 year ago

Yep, this is on the radar, for now waiting for a bit longer, maybe 1-2 weeks to see whether the BA.2.86 common ancestor stays there and for the phylogeny to stabilize.

FedeGueli commented 1 year ago

Yep, this is on the radar, for now waiting for a bit longer, maybe 1-2 weeks to see whether the BA.2.86 common ancestor stays there and for the phylogeny to stabilize.

Yes thx for looking into it, i thought it was good to describe early the tree before it becomes too big to track ( always hard then to do after) So if something shows some advantage we can catch it immediately

Over-There-Is commented 1 year ago

BA.2.86.1> A28795G England/CLIMB-CM7YEUMZ/2023|EPI_ISL_18227401|2023-08-27 USA/CO-CDPHE-41186476/2023|EPI_ISL_18223813|2023-08-19

FedeGueli commented 1 year ago

BA.2.86.1> A28795G England/CLIMB-CM7YEUMZ/2023|EPI_ISL_18227401|2023-08-27 USA/CO-CDPHE-41186476/2023|EPI_ISL_18223813|2023-08-19

Thx added!

Over-There-Is commented 1 year ago

No, there is no T21610C branch. It is just an inaccurate presentation of ins21608TC.... The original nucleotides are ...GTGTGTTAA... there, and after insertion, they become ...GTGTGTCAT..., and sometimes there will be a missing section, and they will become ...GTGTGTCAN... and get analyzed as T21610C. USA/CO-CDPHE-41186476/2023|EPI_ISL_18223813|2023-08-19 is BA.2.86.1> A28795G> C3811T, C22752T and England/CLIMB-CM7YEUMZ/2023|EPI_ISL_18227401|2023-08-27 is BA.2.86.1> A28795G> C2676T, 21612-21640N All the other sequences with T21610C have Ns from 21611 or 21612 to 21640 too.

FedeGueli commented 1 year ago

Thank you very much @Over-There-Is i stop this here! we will see soon which ones spread the fast. This could be kept as archive of early branches that usually when a lineages grow over 5000 is hard to track back.