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XEC + S:G252S on the ORF1a:A599T branch (39 in 17 places 6 countries ) #1993

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Fearuncle opened this issue Sep 8, 2024 · 15 comments
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XEC + S:G252S on the ORF1a:A599T branch (39 in 17 places 6 countries ) #1993

Fearuncle opened this issue Sep 8, 2024 · 15 comments
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designated S:252 XEC
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XEC.12

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@Fearuncle
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Fearuncle commented Sep 8, 2024 •
edited by FedeGueli
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image
image
tree: https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_25d52_d09b10.json?f_userOrOld=uploaded%20sample

First Seq: 2024-08-12
Most Recent: 2024-08-20

Gisaid: G22316A, T25039C,T3565C

EPI_ISL_19378281 EPI_ISL_19375825 PQ277301.1 PQ277106.1
@FedeGueli
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Query edited to exclude bat viruses: G22316A, T25039C,T3565C

@FedeGueli
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252V 253G were the defining of the two main XBB branches while not relevant until now in JN.1, lets see what this will do.

@Fearuncle Fearuncle changed the title XEC + S:G252S on the ORF1a:A599T branch (4 in 3 countries) XEC + S:G252S on the ORF1a:A599T branch (6 in 3 countries) Sep 13, 2024
@FedeGueli FedeGueli changed the title XEC + S:G252S on the ORF1a:A599T branch (6 in 3 countries) XEC + S:G252S on the ORF1a:A599T branch (6 in 3 countries, only 3 on Gisaid) Sep 17, 2024
@xz-keg
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xz-keg commented Sep 20, 2024 •
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6 on GISAID now, including one GBW from China.

@FedeGueli FedeGueli changed the title XEC + S:G252S on the ORF1a:A599T branch (6 in 3 countries, only 3 on Gisaid) XEC + S:G252S on the ORF1a:A599T branch (6 in 3 countries) Sep 20, 2024
@Fearuncle Fearuncle changed the title XEC + S:G252S on the ORF1a:A599T branch (6 in 3 countries) XEC + S:G252S on the ORF1a:A599T branch (8 in 3 countries) Sep 21, 2024
@xz-keg xz-keg mentioned this issue Sep 25, 2024
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@FedeGueli FedeGueli changed the title XEC + S:G252S on the ORF1a:A599T branch (8 in 3 countries) XEC + S:G252S on the ORF1a:A599T branch (8 in 3 countries - 6 on Gisaid) Sep 25, 2024
@Fearuncle Fearuncle changed the title XEC + S:G252S on the ORF1a:A599T branch (8 in 3 countries - 6 on Gisaid) XEC + S:G252S on the ORF1a:A599T branch (12 in 3 countries - 6 on Gisaid) Sep 26, 2024
@Fearuncle Fearuncle changed the title XEC + S:G252S on the ORF1a:A599T branch (12 in 3 countries - 6 on Gisaid) XEC + S:G252S on the ORF1a:A599T branch (14 in 3 countries - 6 on Gisaid) Oct 1, 2024
@Fearuncle Fearuncle changed the title XEC + S:G252S on the ORF1a:A599T branch (14 in 3 countries - 6 on Gisaid) XEC + S:G252S on the ORF1a:A599T branch (15 in 4 countries - 6 on Gisaid) Oct 2, 2024
@Fearuncle Fearuncle changed the title XEC + S:G252S on the ORF1a:A599T branch (15 in 4 countries - 6 on Gisaid) XEC + S:G252S on the ORF1a:A599T branch (18 in 4 countries - 6 on Gisaid) Oct 3, 2024
@Fearuncle Fearuncle changed the title XEC + S:G252S on the ORF1a:A599T branch (18 in 4 countries - 6 on Gisaid) XEC + S:G252S on the ORF1a:A599T branch (19 in 4 countries - 6 on Gisaid) Oct 5, 2024
@Fearuncle Fearuncle changed the title XEC + S:G252S on the ORF1a:A599T branch (19 in 4 countries - 6 on Gisaid) XEC + S:G252S on the ORF1a:A599T branch (21 in 4 countries - 6 on Gisaid) Oct 10, 2024
@FedeGueli FedeGueli changed the title XEC + S:G252S on the ORF1a:A599T branch (21 in 4 countries - 6 on Gisaid) XEC + S:G252S on the ORF1a:A599T branch (21 in 4 countries - 12 on Gisaid) Oct 10, 2024
@FedeGueli
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12 on Gisaid. @Fearuncle where the other samples not on Gisaid are from?

@xz-keg
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xz-keg commented Oct 12, 2024

13 on GISAID now.

@xz-keg xz-keg changed the title XEC + S:G252S on the ORF1a:A599T branch (21 in 4 countries - 12 on Gisaid) XEC + S:G252S on the ORF1a:A599T branch (21 in 4 countries - 13 on Gisaid) Oct 12, 2024
@Fearuncle Fearuncle changed the title XEC + S:G252S on the ORF1a:A599T branch (21 in 4 countries - 13 on Gisaid) XEC + S:G252S on the ORF1a:A599T branch (22 in 4 countries - 13 on Gisaid) Oct 14, 2024
@Fearuncle
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12 on Gisaid. @Fearuncle where the other samples not on Gisaid are from?

image

@xz-keg
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xz-keg commented Oct 14, 2024 •
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12 on Gisaid. @Fearuncle where the other samples not on Gisaid are from?

image

most are duplicates of same seqs from different platforms.

Better count according to GISAID to avoid duplication, and highlight the non-GISAID seqs that are sure not having a GISAID-backup. (having different collection date etc.)

@xz-keg xz-keg changed the title XEC + S:G252S on the ORF1a:A599T branch (22 in 4 countries - 13 on Gisaid) XEC + S:G252S on the ORF1a:A599T branch (13 in 4 countries ) Oct 14, 2024
@xz-keg xz-keg changed the title XEC + S:G252S on the ORF1a:A599T branch (13 in 4 countries ) XEC + S:G252S on the ORF1a:A599T branch (16 in 4 countries ) Oct 23, 2024
@FedeGueli FedeGueli added the Apparently slow It means that a lineage is accumulating sequences slowly not that it is intrinsically slow. label Oct 28, 2024
@FedeGueli
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It seems slow

@FedeGueli FedeGueli changed the title XEC + S:G252S on the ORF1a:A599T branch (16 in 4 countries ) XEC + S:G252S on the ORF1a:A599T branch (18 in 4 countries ) Nov 2, 2024
@FedeGueli
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Local an d slow closing it

@FedeGueli FedeGueli closed this as not planned Won't fix, can't repro, duplicate, stale Nov 4, 2024
@Over-There-Is
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32 now

@Over-There-Is
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Sweden, Denmark, UK, Canada, US(including 1 from HKSAR)

@FedeGueli FedeGueli changed the title XEC + S:G252S on the ORF1a:A599T branch (18 in 4 countries ) XEC + S:G252S on the ORF1a:A599T branch (32 in 17 places 6 countries ) Nov 22, 2024
@FedeGueli FedeGueli reopened this Nov 22, 2024
@FedeGueli
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Sweden, Denmark, UK, Canada, US(including 1 from HKSAR)

Thx revived quite well , >reopened it.

@xz-keg xz-keg changed the title XEC + S:G252S on the ORF1a:A599T branch (32 in 17 places 6 countries ) XEC + S:G252S on the ORF1a:A599T branch (33 in 17 places 6 countries ) Nov 25, 2024
@Fearuncle Fearuncle changed the title XEC + S:G252S on the ORF1a:A599T branch (33 in 17 places 6 countries ) XEC + S:G252S on the ORF1a:A599T branch (36 in 17 places 6 countries ) Dec 8, 2024
@xz-keg
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xz-keg commented Dec 8, 2024 •
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39 now,I think worth proposal @FedeGueli

@xz-keg xz-keg changed the title XEC + S:G252S on the ORF1a:A599T branch (36 in 17 places 6 countries ) XEC + S:G252S on the ORF1a:A599T branch (39 in 17 places 6 countries ) Dec 8, 2024
@xz-keg xz-keg removed the Apparently slow It means that a lineage is accumulating sequences slowly not that it is intrinsically slow. label Dec 8, 2024
@FedeGueli
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yes please @Fearuncle propose it

39 now,I think worth proposal

@Fearuncle Fearuncle mentioned this issue Dec 9, 2024
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@FedeGueli FedeGueli added this to the XEC.12 milestone Dec 10, 2024
@FedeGueli
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Designated XEC.12 via cov-lineages/pango-designation@58afeb2

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