Remove XBC from list of new clades

nextstrain · Aug 7, 2023 · f745a10 · f745a10
1 parent 69345ba
commit f745a10
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Showing 6 changed files with 66 additions and 74 deletions.
diff --git a/defaults/clade_display_names.yml b/defaults/clade_display_names.yml
@@ -31,8 +31,7 @@
 22F: 22F (XBB)
 23A: 23A (XBB.1.5)
 23B: 23B (XBB.1.16)
-23C: 23C (XBC)
-23D: 23D (CH.1.1)
-23E: 23E (XBB.1.9)
-23F: 23F (XBB.2.3)
-23G: 23G (EG.5)
+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
@@ -33,8 +33,7 @@ Nextstrain_clade	first_sequence
 22F	2022-07-01
 23A	2022-10-01
 23B	2022-11-01
-23C	2022-07-01
-23D	2022-06-01
-23E	2022-08-01
-23F	2022-10-01
-23G	2022-12-01
+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
@@ -31,8 +31,7 @@ clade	parent	WHO
 22F	21L	Omicron
 23A	22F	Omicron
 23B	22F	Omicron
-23C	20A	Delta/Omicron
-23D	22D	Omicron
+23C	22D	Omicron
+23D	22F	Omicron
 23E	22F	Omicron
-23F	22F	Omicron
-23G	23E	Omicron
+23F	23D	Omicron
diff --git a/defaults/clades.tsv b/defaults/clades.tsv
@@ -181,33 +181,26 @@ clade	gene	site	alt
 23B	nuc	18703	T
 23B	nuc	28447	G
 
-23C	clade	20A
-23C	nuc	7091	A
-23C	nuc	21635	T
-23C	nuc	23670	T
-23C	nuc	27898	C
-23C	nuc	27718	C
-
-23D	clade	22D
-23D	nuc	3857	A
-23D	nuc	20741	G
-23D	nuc	22599	C
-23D	nuc	22917	G
-23D	nuc	22893	C
-23D	nuc	23019	C
+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	5720	A
-23E	nuc	12789	T
-23E	nuc	28297	C
-
-23F	clade	22F
-23F	nuc	4234	T
-23F	nuc	23123	T
-23F	nuc	27431	T
-
-23G	clade	23E
-23G	nuc	2334	T
-23G	nuc	9693	T
-23G	nuc	22480	T
-23G	nuc	22930	A
+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
diff --git a/defaults/color_ordering.tsv b/defaults/color_ordering.tsv
@@ -34031,18 +34031,18 @@ clade_membership	22E (BQ.1)
 clade_membership	22F (XBB)
 clade_membership	23A (XBB.1.5)
 clade_membership	23B (XBB.1.16)
-clade_membership	23C (XBC)
-clade_membership	23D (CH.1.1)
-clade_membership	23E (XBB.1.9)
-clade_membership	23F (XBB.2.3)
-clade_membership	23G (EG.5)
+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	XAY
+emerging_lineage	XBC
 emerging_lineage	XBB.1.9.1
 emerging_lineage	XBB.1.42
 emerging_lineage	XBB.1.22.1

diff --git a/defaults/emerging_lineages.tsv b/defaults/emerging_lineages.tsv
@@ -181,36 +181,31 @@ clade	gene	site	alt
 23B	nuc	18703	T
 23B	nuc	28447	G
 
-23C	clade	20A
-23C	nuc	7091	A
-23C	nuc	21635	T
-23C	nuc	23670	T
-23C	nuc	27898	C
-23C	nuc	27718	C
-
-23D	clade	22D
-23D	nuc	3857	A
-23D	nuc	20741	G
-23D	nuc	22599	C
-23D	nuc	22917	G
-23D	nuc	22893	C
-23D	nuc	23019	C
+
+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	5720	A
-23E	nuc	12789	T
-23E	nuc	28297	C
+23E	nuc	4234	T
+23E	nuc	23123	T
+23E	nuc	27431	T
 
-23F	clade	22F
-23F	nuc	4234	T
-23F	nuc	23123	T
-23F	nuc	27431	T
+23F	clade	23D
+23F	nuc	2334	T
+23F	nuc	9693	T
+23F	nuc	22480	T
+23F	nuc	22930	A
 
-23G	clade	23E
-23G	nuc	2334	T
-23G	nuc	9693	T
-23G	nuc	22480	T
-23G	nuc	22930	A
 
 BA.2.3.20	clade	21L
 BA.2.3.20	nuc	6770	G
@@ -223,6 +218,13 @@ BN.1	nuc	22599	C
 BN.1	nuc	22629	C
 BN.1	nuc	23031	C
 
+XBC	clade	20A
+XBC	nuc	23670	T
+XBC	nuc	27898	C
+XBC	nuc	21635	T
+XBC	nuc	27718	C
+XBC	nuc	7091	A
+
 XAY	clade	20A
 XAY	nuc	12163	A
 XAY	nuc	21618	G
@@ -236,7 +238,7 @@ FE.1	nuc	3662	G
 FE.1	nuc	8001	G
 FE.1	nuc	26012	G
 
-XBB.1.9.1	clade	23E
+XBB.1.9.1	clade	23D
 XBB.1.9.1	nuc	11956	T
 XBB.1.9.1	nuc	23018	C