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Designate clades 23G (XBB.1.5.70), 23H (HK.3), 23I (BA.2.86) #1087

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merged 2 commits into from
Nov 30, 2023
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Designate clades 23G (XBB.1.5.70), 23H (HK.3), 23I (BA.2.86) #1087

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b2bda2d
Designate clades 23G (XBB.1.5.70), 23H (HK.3), 23I (BA.2.86)
corneliusroemer Nov 29, 2023
094cf7c
fix: missing closing paren in color ordering
corneliusroemer Nov 29, 2023
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3 changes: 3 additions & 0 deletions defaults/clade_display_names.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -35,3 +35,6 @@
23D: 23D (XBB.1.9)
23E: 23E (XBB.2.3)
23F: 23F (EG.5.1)
23G: 23G (XBB.1.5.70)
23H: 23H (HK.3)
23I: 23I (BA.2.86)
3 changes: 3 additions & 0 deletions defaults/clade_emergence_dates.tsv
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Original file line number Diff line number Diff line change
Expand Up @@ -37,3 +37,6 @@ Nextstrain_clade first_sequence
23D 2022-08-01
23E 2022-10-01
23F 2023-01-01
23G 2023-01-01
23H 2023-03-01
23I 2023-04-01
3 changes: 3 additions & 0 deletions defaults/clade_hierarchy.tsv
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Original file line number Diff line number Diff line change
Expand Up @@ -35,3 +35,6 @@ clade parent WHO
23D 22F Omicron
23E 22F Omicron
23F 23D Omicron
23G 23A Omicron
23H 23F Omicron
23I 21L Omicron
14 changes: 14 additions & 0 deletions defaults/clades.tsv
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Original file line number Diff line number Diff line change
Expand Up @@ -205,3 +205,17 @@ clade gene site alt
23F nuc 21718 T
23F nuc 22480 T
23F nuc 22930 A

23G clade 23A
23G nuc 8737 C
23G nuc 25045 G
23G nuc 28005 T

23H clade 23F
23H nuc 13627 A
23H nuc 22927 T

23I clade 21L
23I nuc 897 A
23I nuc 15756 A
23I nuc 28958 A
9 changes: 6 additions & 3 deletions defaults/color_ordering.tsv
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Original file line number Diff line number Diff line change
Expand Up @@ -34035,6 +34035,9 @@ clade_membership 23C (CH.1.1)
clade_membership 23D (XBB.1.9)
clade_membership 23E (XBB.2.3)
clade_membership 23F (EG.5.1)
clade_membership 23G (XBB.1.5.70)
clade_membership 23H (HK.3)
clade_membership 23I (BA.2.86)

################

Expand All @@ -34049,13 +34052,13 @@ emerging_lineage XBB.1.22.1
emerging_lineage XBB.1.17.1
emerging_lineage FE.1
emerging_lineage FL.1.5.1
emerging_lineage XBB.1.5.70
emerging_lineage XBB.1.16.6
emerging_lineage DV.7.1
emerging_lineage HV.1
emerging_lineage HK.3
emerging_lineage BA.2.86
emerging_lienage GW.5
emerging_lineage JD.1
emerging_lineage XBB.1.41
emerging_lineage JN.1

################

Expand Down
40 changes: 26 additions & 14 deletions defaults/emerging_lineages.tsv
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Original file line number Diff line number Diff line change
Expand Up @@ -206,6 +206,20 @@ clade gene site alt
23F nuc 22480 T
23F nuc 22930 A

23G clade 23A
23G nuc 8737 C
23G nuc 25045 G
23G nuc 28005 T

23H clade 23F
23H nuc 13627 A
23H nuc 22927 T

23I clade 21L
23I nuc 897 A
23I nuc 15756 A
23I nuc 28958 A


BA.2.3.20 clade 21L
BA.2.3.20 nuc 6770 G
Expand Down Expand Up @@ -265,11 +279,6 @@ FL.1.5.1 nuc 3242 A
FL.1.5.1 nuc 20060 T
FL.1.5.1 nuc 22995 G

XBB.1.5.70 clade 23A
XBB.1.5.70 nuc 8737 C
XBB.1.5.70 nuc 25045 G
XBB.1.5.70 nuc 28005 T

XBB.1.16.6 clade 23B
XBB.1.16.6 nuc 12397 G
XBB.1.16.6 nuc 8947 T
Expand All @@ -285,19 +294,22 @@ HV.1 nuc 5835 T
HV.1 nuc 22033 A
HV.1 nuc 22917 G

HK.3 clade 23F
HK.3 nuc 13627 A
HK.3 nuc 22927 T

BA.2.86 clade 21L
BA.2.86 nuc 15756 A
BA.2.86 nuc 897 A
BA.2.86 nuc 28958 A

GW.5 clade 22F
GW.5 nuc 1170 T
GW.5 nuc 6501 A
GW.5 nuc 10042 G
GW.5 nuc 21363 T
GW.5 nuc 27915 G

JD.1 clade 23A
JD.1 nuc 14634 G
JD.1 nuc 22927 T
JD.1 nuc 22928 C

XBB.1.41 clade 22F
XBB.1.41 nuc 1473 T
XBB.1.41 nuc 20102 T

JN.1 clade 23I
JN.1 nuc 11727 A
JN.1 nuc 22926 C