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XBB.1.16 plus S:Q613H and N:S412N ( 61 sequences ) #54

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FedeGueli opened this issue May 13, 2023 · 3 comments
Closed

XBB.1.16 plus S:Q613H and N:S412N ( 61 sequences ) #54

FedeGueli opened this issue May 13, 2023 · 3 comments
Labels
Convergent evolution Lineages with convergent mutations designated S:613
Milestone
XBB.1.16.16

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@FedeGueli
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I noticed that XBB.1.16 has acquired S:Q613H in multiple branches.
The biggest of them interestingly has 3 sub branch all defined by N mutations so it shows S:Q613H coupled with N mutation as in EG.1.

Tree:
https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_126d5_fddbc0.json?c=userOrOld&label=id:node_6700694
Schermata 2023-05-13 alle 21 02 35

Being impossible to say if the three subbranches are really sibling or it is just the fact that Usher collects here lineages stemming directly from the politomy with S:Q613H

So here i want to propose the biggest branch on the top defined by S:Q613H then N:S412N

Defining mutations:
XBB.1.16 >> S:Q613H (G23401T) > N:S412N (G29508A)

Gisaid query : G23401T,T12730A, G29508A

Sequences : 19

Samples: EPI_ISL_17428133, EPI_ISL_17497068, EPI_ISL_17497187,
EPI_ISL_17497192, EPI_ISL_17497198, EPI_ISL_17586431,
EPI_ISL_17586527, EPI_ISL_17586567, EPI_ISL_17586713,
EPI_ISL_17586811, EPI_ISL_17591702, EPI_ISL_17595780,
EPI_ISL_17595798, EPI_ISL_17595801, EPI_ISL_17621219,
EPI_ISL_17627050, EPI_ISL_17651328, EPI_ISL_17651355,
EPI_ISL_17651554
@FedeGueli FedeGueli added the Convergent evolution Lineages with convergent mutations label May 13, 2023
@FedeGueli FedeGueli changed the title XBB.1.16 plus S:Q613H and N:S412N ( 19sequences ) XBB.1.16 plus S:Q613H and N:S412N ( 21 sequences ) May 24, 2023
@FedeGueli
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slow

@FedeGueli FedeGueli closed this as not planned Won't fix, can't repro, duplicate, stale May 30, 2023
@FedeGueli FedeGueli changed the title XBB.1.16 plus S:Q613H and N:S412N ( 21 sequences ) XBB.1.16 plus S:Q613H and N:S412N ( 39 sequences ) Jun 26, 2023
@FedeGueli
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After an apparent hyatus this seems circulating outside India with some sequences collected in June. Not sure how fast it is but better tracking it.

@FedeGueli FedeGueli reopened this Jun 26, 2023
@FedeGueli FedeGueli changed the title XBB.1.16 plus S:Q613H and N:S412N ( 39 sequences ) XBB.1.16 plus S:Q613H and N:S412N ( 46 sequences ) Jul 2, 2023
@FedeGueli FedeGueli added S:613 Apparently slow It means that a lineage is accumulating sequences slowly not that it is intrinsically slow. labels Jul 2, 2023
@FedeGueli FedeGueli changed the title XBB.1.16 plus S:Q613H and N:S412N ( 46 sequences ) XBB.1.16 plus S:Q613H and N:S412N ( 47 sequences ) Jul 5, 2023
@FedeGueli FedeGueli changed the title XBB.1.16 plus S:Q613H and N:S412N ( 47 sequences ) XBB.1.16 plus S:Q613H and N:S412N ( 52 sequences ) Jul 9, 2023
@FedeGueli FedeGueli changed the title XBB.1.16 plus S:Q613H and N:S412N ( 52 sequences ) XBB.1.16 plus S:Q613H and N:S412N ( 61 sequences ) Jul 13, 2023
@FedeGueli FedeGueli removed the Apparently slow It means that a lineage is accumulating sequences slowly not that it is intrinsically slow. label Jul 13, 2023
@NkRMnZr NkRMnZr mentioned this issue Jul 13, 2023
Closed
FedeGueli referenced this issue in cov-lineages/pango-designation Jul 14, 2023
@corneliusroemer
Designate XBB.1.16.16 (S:Q613H, S:S412N, India-GJ/USA/Pakistan) with …
df3436b 
…60 seqs
@FedeGueli
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Now this is XBB.1.16.16

FedeGueli added a commit to FedeGueli/pango-designation that referenced this issue Jul 17, 2023
@FedeGueli
Update lineage_notes.txt
913d17a 
add sars-cov-2-variants/lineage-proposals#54 to XBB.1.16.16
add sars-cov-2-variants/lineage-proposals#208 to XBB.1.49
add cov-lineages#2083 to HF.1
add  cov-lineages#2093 to GK.1.2
add sars-cov-2-variants/lineage-proposals#363 to HD.1
add  cov-lineages#1832 to FU.4
@FedeGueli FedeGueli mentioned this issue Jul 17, 2023
Merged
corneliusroemer added a commit to cov-lineages/pango-designation that referenced this issue Jul 17, 2023
@FedeGueli @corneliusroemer
Update lineage_notes.txt (#2104)
feb1127 
add sars-cov-2-variants/lineage-proposals#54 to XBB.1.16.16
add sars-cov-2-variants/lineage-proposals#208 to XBB.1.49
add #2083 to HF.1
add  #2093 to GK.1.2
add sars-cov-2-variants/lineage-proposals#363 to HD.1
add  #1832 to FU.4

Co-authored-by: Cornelius Roemer <cornelius.roemer@gmail.com>
@aviczhl2 aviczhl2 added this to the XBB.1.16.16 milestone Dec 17, 2023
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