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Multiple lineages with multiple AA deletions around 184-190, 6 branches as of Aug 21 #1798

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FedeGueli opened this issue Jul 30, 2024 · 14 comments
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Multiple lineages with multiple AA deletions around 184-190, 6 branches as of Aug 21 #1798

FedeGueli opened this issue Jul 30, 2024 · 14 comments
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Apparently slow It means that a lineage is accumulating sequences slowly not that it is intrinsically slow. Deletions between S:180-190 it is an umbrella that collects lineages with mutations in the S:180-190 area of the NTD Deletions/Truncations/Frameshifted Lineage showing any deletions or stop codons or TRS changes. Multiple lineages

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@FedeGueli
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FedeGueli commented Jul 30, 2024 •
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It seems that in this phase of the pandemic deletions around 184-190 could be convergently beneficial.
We are used to the S:N185del+S:F186I recurrent deletion (As GE.1) or we have already observed large deletion in that area but it usually happened between 180-184 (as XBB.1.5.103) .
Now we have already two lineages designated with it LS.1 and JN.1.7.8 and one proposed in #1703 but more are popping up.

  1. LS.1 Query: G9049A,G3085T, T21644C Samples: 30
  2. JN.1.7.8 Query:C29367T,C2695T,C7840T,T22930A Samples: 69
    with a Trio sub: C16954T,del22115,T3565C Samples:5 ( tracked as Br 155 of Multiple JN.1 + S:R346X + FliRT + Trio : 155 branches as July 30 #1089)
  3. KR.1 + 186-89del+190W dead Query:del22118_22129,C1762A Samples: 13 proposed in KR.1 got S:186-189del resulting in S:R190W ( S:F186W plus S:187-190del for Gisaid) (14 seqs, 5 states, 3 continents) #1703
  4. KP.3.2.4 + 186-189del Query: C15654T, C21516T,del22115 Samples:3 dead
  5. LB.1.4 +186-189del and 176F : A10018G,del22115 Samples: 2 dead
  6. LB.1.7 + 186-189del Query: C4784T,del22115,G21123T Samples:40 proposed in # 2797 pango
  7. JN.1.16.1 + 186-189del Query: del22115,C7072T, C9803T Samples: 10 dead
  8. KP.2.3 + 185-189del proposed in KP.2.3 subbranch with S:del185-189(21 sequences, 3 countries) 8% in Chile in September #2003
@FedeGueli FedeGueli changed the title Multiple lineages with multiple AA deletions around 184-190 Multiple lineages with multiple AA deletions around 184-190, 7 branches as of July 30 Jul 30, 2024
@FedeGueli FedeGueli changed the title Multiple lineages with multiple AA deletions around 184-190, 7 branches as of July 30 Multiple lineages with multiple AA deletions around 184-190, 6 branches as of July 30 Jul 30, 2024
@georg122
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georg122 commented Aug 3, 2024

In what way beneficial?

@FedeGueli
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In what way beneficial?

adding some growth advantage.

@FedeGueli FedeGueli added Deletions between S:180-190 it is an umbrella that collects lineages with mutations in the S:180-190 area of the NTD and removed S:187 S:186 S:188 S:185 S:184 S:189 labels Aug 4, 2024
@FedeGueli
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Br.6 goes to 12
Br.7 to 6

@FedeGueli
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Br.6 went to 14
Br.4 to 3

they doesnt seem fast

@FedeGueli FedeGueli changed the title Multiple lineages with multiple AA deletions around 184-190, 6 branches as of July 30 Multiple lineages with multiple AA deletions around 184-190, 6 branches as of Aug 21 Aug 22, 2024
@FedeGueli
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Br.6 now 18
Br.7 now 8

@FedeGueli
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+1 each br.6 and br.7

@Mydtlwn
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Mydtlwn commented Sep 10, 2024

#2003

@FedeGueli
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Added branch 8 from #2003,

branch 6 is now 25, maybe worth proposing it? cc @aviczhl2 @Over-There-Is @NkRMnZr ?

branch 7 is 10 growing slowly

@FedeGueli
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only branch 6 is still going , now at 27

@FedeGueli FedeGueli added the Apparently slow It means that a lineage is accumulating sequences slowly not that it is intrinsically slow. label Sep 17, 2024
@FedeGueli
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Branch 6 is the only alive 33 samples with the last samples from different US states. Leaving it open for a while

@FedeGueli
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FedeGueli commented Sep 26, 2024 •
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Br 6 now 35, @aviczhl2 what about if i propose br.6 and close this? i m unsure BR.6 can compete but it is still growng so maybe worth being tracked

@xz-keg
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xz-keg commented Sep 26, 2024

Br 6 now 35, @aviczhl2 what about if i propose br.6 and close this? i m unsure BR.6 can compete but it is still growng so maybe worth being tracked

Yeah sure.

@FedeGueli
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Br 6 now 35, @aviczhl2 what about if i propose br.6 and close this? i m unsure BR.6 can compete but it is still growng so maybe worth being tracked

Yeah sure.

i will wait a week more i suspect this wll stop growing as the most of lineages as of today

@FedeGueli
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Br.6 up to 39 proposing it and closing this

@FedeGueli FedeGueli closed this as not planned Won't fix, can't repro, duplicate, stale Oct 3, 2024
@FedeGueli FedeGueli mentioned this issue Oct 3, 2024
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Apparently slow It means that a lineage is accumulating sequences slowly not that it is intrinsically slow. Deletions between S:180-190 it is an umbrella that collects lineages with mutations in the S:180-190 area of the NTD Deletions/Truncations/Frameshifted Lineage showing any deletions or stop codons or TRS changes. Multiple lineages
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@xz-keg @Mydtlwn @FedeGueli @georg122