Merge pull request #1078 from nextstrain/new-clades-2023-08

Designate 4 new clades: CH.1.1 -> 23C, XBB.1.9 -> 23D, XBB.2.3 -> 23E, EG.5.1 (XBB.1.9.2.5.1) -> 23F
nextstrain · Aug 9, 2023 · d34a0cf · d34a0cf
2 parents 851045c + 168c6c0
commit d34a0cf
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Showing 6 changed files with 70 additions and 37 deletions.
diff --git a/defaults/clade_display_names.yml b/defaults/clade_display_names.yml
@@ -31,3 +31,7 @@
 22F: 22F (XBB)
 23A: 23A (XBB.1.5)
 23B: 23B (XBB.1.16)
+23C: 23C (CH.1.1)
+23D: 23D (XBB.1.9)
+23E: 23E (XBB.2.3)
+23F: 23F (EG.5.1)
diff --git a/defaults/clade_emergence_dates.tsv b/defaults/clade_emergence_dates.tsv
@@ -30,6 +30,10 @@ Nextstrain_clade	first_sequence
 22C	2021-12-01
 22D	2022-04-01
 22E	2022-07-10
-22F	2022-08-01
+22F	2022-07-01
 23A	2022-10-01
 23B	2022-11-01
+23C	2022-06-01
+23D	2022-08-01
+23E	2022-10-01
+23F	2023-01-01
diff --git a/defaults/clade_hierarchy.tsv b/defaults/clade_hierarchy.tsv
@@ -31,3 +31,7 @@ clade	parent	WHO
 22F	21L	Omicron
 23A	22F	Omicron
 23B	22F	Omicron
+23C	22D	Omicron
+23D	22F	Omicron
+23E	22F	Omicron
+23F	23D	Omicron
diff --git a/defaults/clades.tsv b/defaults/clades.tsv
@@ -179,4 +179,29 @@ clade	gene	site	alt
 23B	nuc	12730	A
 23B	nuc	14856	G
 23B	nuc	18703	T
-23B	nuc	28447	G
+23B	nuc	28447	G
+
+23C	clade	22D
+23C	nuc	3857	A
+23C	nuc	20741	G
+23C	nuc	22599	C
+23C	nuc	22917	G
+23C	nuc	22893	C
+23C	nuc	23019	C
+
+23D	clade	22F
+23D	nuc	5720	A
+23D	nuc	12789	T
+23D	nuc	28297	C
+
+23E	clade	22F
+23E	nuc	4234	T
+23E	nuc	23123	T
+23E	nuc	27431	T
+
+23F	clade	23D
+23F	nuc	2334	T
+23F	nuc	9693	T
+23F	nuc	21718	T
+23F	nuc	22480	T
+23F	nuc	22930	A
diff --git a/defaults/color_ordering.tsv b/defaults/color_ordering.tsv
@@ -34031,25 +34031,24 @@ clade_membership	22E (BQ.1)
 clade_membership	22F (XBB)
 clade_membership	23A (XBB.1.5)
 clade_membership	23B (XBB.1.16)
+clade_membership	23C (CH.1.1)
+clade_membership	23D (XBB.1.9)
+clade_membership	23E (XBB.2.3)
+clade_membership	23F (EG.5.1)
 
 ################
 
 
 emerging_lineage	BA.2.3.20
 emerging_lineage	BN.1
-emerging_lineage	CH.1.1
 emerging_lineage	XAY
 emerging_lineage	XBC
-emerging_lineage	XBB.1.9
 emerging_lineage	XBB.1.9.1
-emerging_lineage	XBB.1.9.2
-emerging_lineage	EG.5
 emerging_lineage	XBB.1.42
 emerging_lineage	XBB.1.22.1
 emerging_lineage	XBB.1.19
 emerging_lineage	XBB.1.17.1
 emerging_lineage	FE.1
-emerging_lineage	XBB.2.3
 
 ################
 

diff --git a/defaults/emerging_lineages.tsv b/defaults/emerging_lineages.tsv
@@ -181,6 +181,32 @@ clade	gene	site	alt
 23B	nuc	18703	T
 23B	nuc	28447	G
 
+
+23C	clade	22D
+23C	nuc	3857	A
+23C	nuc	20741	G
+23C	nuc	22599	C
+23C	nuc	22917	G
+23C	nuc	22893	C
+23C	nuc	23019	C
+
+23D	clade	22F
+23D	nuc	5720	A
+23D	nuc	12789	T
+23D	nuc	28297	C
+
+23E	clade	22F
+23E	nuc	4234	T
+23E	nuc	23123	T
+23E	nuc	27431	T
+
+23F	clade	23D
+23F	nuc	2334	T
+23F	nuc	9693	T
+23F	nuc	22480	T
+23F	nuc	22930	A
+
+
 BA.2.3.20	clade	21L
 BA.2.3.20	nuc	6770	G
 BA.2.3.20	nuc	22332	A
@@ -207,38 +233,15 @@ XAY	nuc	22899	A
 XAY	nuc	23679	T
 XAY	nuc	27575	G
 
-CH.1.1	clade	22D
-CH.1.1	nuc	3857	A
-CH.1.1	nuc	23019	C
-CH.1.1	nuc	22599	C
-CH.1.1	nuc	20741	G
-CH.1.1	nuc	22893	C
-CH.1.1	nuc	22917	G
-
 FE.1	clade	22F
 FE.1	nuc	3662	G
 FE.1	nuc	8001	G
 FE.1	nuc	26012	G
 
-XBB.1.9	clade	22F
-XBB.1.9	nuc	5720	A
-XBB.1.9	nuc	12789	T
-XBB.1.9	nuc	28297	C
-
-XBB.1.9.1	clade	XBB.1.9
+XBB.1.9.1	clade	23D
 XBB.1.9.1	nuc	11956	T
 XBB.1.9.1	nuc	23018	C
 
-XBB.1.9.2	clade	XBB.1.9
-XBB.1.9.2	nuc	16878	T
-XBB.1.9.2	nuc	23018	C
-XBB.1.9.2	nuc	27507	C
-
-XBB.2.3	clade	22F
-XBB.2.3	nuc	4234	T
-XBB.2.3	nuc	23123	T
-XBB.2.3	nuc	27431	T
-
 XBB.1.22.1	clade	22F
 XBB.1.22.1	nuc	22161	G
 XBB.1.22.1	nuc	23018	C
@@ -262,9 +265,3 @@ XBB.1.19	nuc	10042	G
 XBB.1.19	nuc	21363	T
 XBB.1.19	nuc	23018	C
 XBB.1.19	nuc	27915	G
-
-EG.5	clade	XBB.1.9.2
-EG.5	nuc	2334	T
-EG.5	nuc	9693	T
-EG.5	nuc	22480	T
-EG.5	nuc	22930	A