Merge pull request #1087 from nextstrain/clades-2023-11

Designate clades 23G (XBB.1.5.70), 23H (HK.3), 23I (BA.2.86)
nextstrain · Nov 30, 2023 · 9ddcaba · 9ddcaba
2 parents a29a3b2 + 094cf7c
commit 9ddcaba
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Showing 6 changed files with 55 additions and 17 deletions.
diff --git a/defaults/clade_display_names.yml b/defaults/clade_display_names.yml
@@ -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)
diff --git a/defaults/clade_emergence_dates.tsv b/defaults/clade_emergence_dates.tsv
@@ -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
diff --git a/defaults/clade_hierarchy.tsv b/defaults/clade_hierarchy.tsv
@@ -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
diff --git a/defaults/clades.tsv b/defaults/clades.tsv
@@ -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
diff --git a/defaults/color_ordering.tsv b/defaults/color_ordering.tsv
@@ -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)
 
 ################
 
@@ -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
 
 ################
 

diff --git a/defaults/emerging_lineages.tsv b/defaults/emerging_lineages.tsv
@@ -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
@@ -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
@@ -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