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XBB.2.3+S:210del,N:A267S(151 seqs, 17 countries) and its further sublineage Orf7a:Q90*,Orf9b:T72I with ~15% prevalence in Bangladesh (39 seqs) #328

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aviczhl2 opened this issue Jul 5, 2023 · 15 comments
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XBB.2.3+S:210del,N:A267S(151 seqs, 17 countries) and its further sublineage Orf7a:Q90*,Orf9b:T72I with ~15% prevalence in Bangladesh (39 seqs) #328

aviczhl2 opened this issue Jul 5, 2023 · 15 comments
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Apparently slow It means that a lineage is accumulating sequences slowly not that it is intrinsically slow. Broadened designated High local prevalence Lineage that apparently gained high prevalence in one country or region Truncated Orf(3-10)
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XBB.2.3.20

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@aviczhl2
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aviczhl2 commented Jul 5, 2023 •
edited

XBB.2.3+T18882C,T27992A,G29072T(N:A267S), del22190_22192(S:210del)+C27661T(Orf7a:Q90*) ,C28498T(Orf9b:T72I)

GISAID query: C27661T,C28498T,G29072T

GISAID query for S:210del, N:A267S: del22190_22192, T27992A

No. of seqs: 23(Bangladesh 9 China 2 USA 5(1 from UAE), Thailand 1 Israel 1 Malaysia 1 Australia 1 UK 3)

First: EPI_ISL_17208395, Israel, 2023-2-20
Latest: EPI_ISL_17850929 ,China, 2023-6-18

Note that it represents 9/57 of Bangladesh seqs from 2023-4-15.

usher
屏幕截图 2023-07-05 162855
@FedeGueli FedeGueli added Truncated Orf(3-10) Mutations outside spike High local prevalence Lineage that apparently gained high prevalence in one country or region labels Jul 5, 2023
@aviczhl2
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aviczhl2 commented Jul 8, 2023

+1 South Korea

@aviczhl2 aviczhl2 changed the title XBB.2.3+N:A267S+Orf7a:Q90*,Orf9b:T72I with ~15% prevalence in Bangladesh (23 seqs, 9 countries) XBB.2.3+N:A267S+Orf7a:Q90*,Orf9b:T72I with ~15% prevalence in Bangladesh (24 seqs, 10 countries) Jul 8, 2023
@aviczhl2 aviczhl2 changed the title XBB.2.3+N:A267S+Orf7a:Q90*,Orf9b:T72I with ~15% prevalence in Bangladesh (24 seqs, 10 countries) XBB.2.3+N:A267S+Orf7a:Q90*,Orf9b:T72I with ~15% prevalence in Bangladesh (26 seqs, 10 countries) Jul 9, 2023
@aviczhl2
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aviczhl2 commented Jul 9, 2023

2/20 in today's Bangladesh batch

@aviczhl2 aviczhl2 changed the title XBB.2.3+N:A267S+Orf7a:Q90*,Orf9b:T72I with ~15% prevalence in Bangladesh (26 seqs, 10 countries) XBB.2.3+N:A267S+Orf7a:Q90*,Orf9b:T72I with ~15% prevalence in Bangladesh (27 seqs, 10 countries) Jul 11, 2023
@aviczhl2 aviczhl2 changed the title XBB.2.3+N:A267S+Orf7a:Q90*,Orf9b:T72I with ~15% prevalence in Bangladesh (27 seqs, 10 countries) XBB.2.3+N:A267S+Orf7a:Q90*,Orf9b:T72I with ~15% prevalence in Bangladesh (28 seqs, 10 countries) Jul 14, 2023
@FedeGueli
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Waiting for the next upload from B.

@aviczhl2
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Edited the GISAID query to cover some T18882Y seqs from Singapore. 34 seqs now.

@aviczhl2 aviczhl2 changed the title XBB.2.3+N:A267S+Orf7a:Q90*,Orf9b:T72I with ~15% prevalence in Bangladesh (28 seqs, 10 countries) XBB.2.3+N:A267S+Orf7a:Q90*,Orf9b:T72I with ~15% prevalence in Bangladesh (34 seqs, 11 countries) Jul 24, 2023
@aviczhl2 aviczhl2 mentioned this issue Jul 26, 2023
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@aviczhl2 aviczhl2 changed the title XBB.2.3+N:A267S+Orf7a:Q90*,Orf9b:T72I with ~15% prevalence in Bangladesh (34 seqs, 11 countries) XBB.2.3+N:A267S+Orf7a:Q90*,Orf9b:T72I with ~15% prevalence in Bangladesh (37 seqs, 11 countries) Jul 29, 2023
@aviczhl2
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aviczhl2 commented Aug 1, 2023

+1 France

@aviczhl2 aviczhl2 changed the title XBB.2.3+N:A267S+Orf7a:Q90*,Orf9b:T72I with ~15% prevalence in Bangladesh (37 seqs, 11 countries) XBB.2.3+N:A267S+Orf7a:Q90*,Orf9b:T72I with ~15% prevalence in Bangladesh (38 seqs, 12 countries) Aug 1, 2023
@aviczhl2 aviczhl2 mentioned this issue Aug 4, 2023
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@aviczhl2 aviczhl2 changed the title XBB.2.3+N:A267S+Orf7a:Q90*,Orf9b:T72I with ~15% prevalence in Bangladesh (38 seqs, 12 countries) XBB.2.3+S:210del,N:A267S+Orf7a:Q90*,Orf9b:T72I with ~15% prevalence in Bangladesh (38 seqs, 12 countries) Aug 4, 2023
@aviczhl2
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aviczhl2 commented Aug 4, 2023

@FedeGueli I just realized that this lineage also has S:210del and is the XBB.2.3-side donor of #535.

@FedeGueli
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@FedeGueli I just realized that this lineage also has S:210del and is the XBB.2.3-side donor of #535.
Wow! great! i have thought of this one but didnt check then!
cc @ryhisner !!! @aviczhl2 found and proposed already the donor!

@aviczhl2
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aviczhl2 commented Aug 10, 2023 •
edited

I check the tree and found that the S:210del comes alongside with N:267S. @FedeGueli

Uploaded are seqs with S:210del.
image

I'd like to boarden the proposal to S:210del, N:267S, and this gives 145 seqs and additional countries of India, Ireland, Japan, New Zealand, Malaysia.

Query: del22190_22192, T27992A (Edited)

@aviczhl2 aviczhl2 changed the title XBB.2.3+S:210del,N:A267S+Orf7a:Q90*,Orf9b:T72I with ~15% prevalence in Bangladesh (38 seqs, 12 countries) XBB.2.3+S:210del,N:A267S(145 seqs)+Orf7a:Q90*,Orf9b:T72I with ~15% prevalence in Bangladesh (38 seqs, 12 countries) Aug 10, 2023
@aviczhl2 aviczhl2 changed the title XBB.2.3+S:210del,N:A267S(145 seqs)+Orf7a:Q90*,Orf9b:T72I with ~15% prevalence in Bangladesh (38 seqs, 12 countries) XBB.2.3+S:210del,N:A267S(145 seqs, 17 countries)+Orf7a:Q90*,Orf9b:T72I with ~15% prevalence in Bangladesh (38 seqs) Aug 10, 2023
@FedeGueli
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great work @aviczhl2 thx.

@FedeGueli FedeGueli changed the title XBB.2.3+S:210del,N:A267S(145 seqs, 17 countries)+Orf7a:Q90*,Orf9b:T72I with ~15% prevalence in Bangladesh (38 seqs) XBB.2.3+S:210del,N:A267S(145 seqs, 17 countries) and its further sublineage Orf7a:Q90*,Orf9b:T72I with ~15% prevalence in Bangladesh (38 seqs) Aug 10, 2023
@FedeGueli
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FedeGueli commented Aug 10, 2023 •
edited

i cant find any seqs with that query @aviczhl2 i ll use this one: N_A267S,Spike_I210del,SPike_P521S

@aviczhl2
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i cant find any seqs with that query @aviczhl2 i ll use this one: N_A267S,Spike_I210del

Sorry shall be T27992A, del22190_22192

N_A267S,Spike_I210del includes a few delta seqs.

@FedeGueli
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i cant find any seqs with that query @aviczhl2 i ll use this one: N_A267S,Spike_I210del

thx i ve added also P521S!

@aviczhl2 aviczhl2 changed the title XBB.2.3+S:210del,N:A267S(145 seqs, 17 countries) and its further sublineage Orf7a:Q90*,Orf9b:T72I with ~15% prevalence in Bangladesh (38 seqs) XBB.2.3+S:210del,N:A267S(147 seqs, 17 countries) and its further sublineage Orf7a:Q90*,Orf9b:T72I with ~15% prevalence in Bangladesh (39 seqs) Aug 17, 2023
@aviczhl2 aviczhl2 changed the title XBB.2.3+S:210del,N:A267S(147 seqs, 17 countries) and its further sublineage Orf7a:Q90*,Orf9b:T72I with ~15% prevalence in Bangladesh (39 seqs) XBB.2.3+S:210del,N:A267S(149 seqs, 17 countries) and its further sublineage Orf7a:Q90*,Orf9b:T72I with ~15% prevalence in Bangladesh (39 seqs) Aug 21, 2023
@aviczhl2 aviczhl2 changed the title XBB.2.3+S:210del,N:A267S(149 seqs, 17 countries) and its further sublineage Orf7a:Q90*,Orf9b:T72I with ~15% prevalence in Bangladesh (39 seqs) XBB.2.3+S:210del,N:A267S(151 seqs, 17 countries) and its further sublineage Orf7a:Q90*,Orf9b:T72I with ~15% prevalence in Bangladesh (39 seqs) Sep 2, 2023
@FedeGueli
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it seems to have slowed down a lot. wondering why

@FedeGueli FedeGueli added Apparently slow It means that a lineage is accumulating sequences slowly not that it is intrinsically slow. and removed Mutations outside spike labels Sep 4, 2023
@FedeGueli FedeGueli closed this as not planned Won't fix, can't repro, duplicate, stale Sep 4, 2023
@FedeGueli
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Closing for now better staying focusing on things with advantage. But still this was interesting.

@aviczhl2 aviczhl2 mentioned this issue Sep 7, 2023
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corneliusroemer added a commit to cov-lineages/pango-designation that referenced this issue Oct 15, 2023
@corneliusroemer
Designate XBB.2.3.20 (N:A267S, S:210del, Bangladesh, from sars-cov-2-…
76e2699 
…variants/lineage-proposals#328)

Resolves sars-cov-2-variants/lineage-proposals#328

Beware, this is not BA.2.3.20 even though the numbers are the same
@FedeGueli FedeGueli added this to the XBB.2.3.20 milestone Oct 15, 2023
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Now this is XBB.2.3.20 via cov-lineages/pango-designation@76e2699

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Apparently slow It means that a lineage is accumulating sequences slowly not that it is intrinsically slow. Broadened designated High local prevalence Lineage that apparently gained high prevalence in one country or region Truncated Orf(3-10)
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