From 3eb09e6bbb5daaf420e307761aa7c39a599c79cc Mon Sep 17 00:00:00 2001
From: Cornelius Roemer <cornelius.roemer@gmail.com>
Date: Thu, 11 Jul 2024 22:27:46 +0200
Subject: [PATCH] Designate clade 24C (KP.3) (#1117)

---
 defaults/clade_display_names.yml   |  1 +
 defaults/clade_emergence_dates.tsv |  1 +
 defaults/clade_hierarchy.tsv       |  1 +
 defaults/clades.tsv                |  3 +++
 defaults/color_ordering.tsv        |  5 +++++
 defaults/emerging_lineages.tsv     | 32 ++++++++++++++++++++++++++++++
 6 files changed, 43 insertions(+)

diff --git a/defaults/clade_display_names.yml b/defaults/clade_display_names.yml
index 4aff0a9bc..f550d3437 100644
--- a/defaults/clade_display_names.yml
+++ b/defaults/clade_display_names.yml
@@ -40,3 +40,4 @@
 23I: 23I (BA.2.86)
 24A: 24A (JN.1)
 24B: 24B (JN.1.11.1)
+24C: 24C (KP.3)
diff --git a/defaults/clade_emergence_dates.tsv b/defaults/clade_emergence_dates.tsv
index 94da5c227..0cadee025 100644
--- a/defaults/clade_emergence_dates.tsv
+++ b/defaults/clade_emergence_dates.tsv
@@ -42,3 +42,4 @@ Nextstrain_clade	first_sequence
 23I	2023-04-01
 24A	2023-07-01
 24B	2023-11-01
+24C	2023-12-01
diff --git a/defaults/clade_hierarchy.tsv b/defaults/clade_hierarchy.tsv
index 66a3d25bc..32e60b1f7 100644
--- a/defaults/clade_hierarchy.tsv
+++ b/defaults/clade_hierarchy.tsv
@@ -40,3 +40,4 @@ clade	parent	WHO
 23I	21L	Omicron
 24A	23I	Omicron
 24B	24A	Omicron
+24C	24B	Omicron
diff --git a/defaults/clades.tsv b/defaults/clades.tsv
index ad468d263..c230791de 100644
--- a/defaults/clades.tsv
+++ b/defaults/clades.tsv
@@ -230,3 +230,6 @@ clade	gene	site	alt
 24B	nuc	17334	T
 24B	nuc	22928	C
 24B	nuc	24872	T
+
+24C	clade	24B
+24C	nuc	23039	G
diff --git a/defaults/color_ordering.tsv b/defaults/color_ordering.tsv
index 7c8e7cd3e..389b60a56 100644
--- a/defaults/color_ordering.tsv
+++ b/defaults/color_ordering.tsv
@@ -34040,6 +34040,7 @@ clade_membership	23H (HK.3)
 clade_membership	23I (BA.2.86)
 clade_membership	24A (JN.1)
 clade_membership	24B (JN.1.11.1)
+clade_membership	24C (KP.3)
 
 ################
 
@@ -34060,6 +34061,10 @@ emerging_lineage	HV.1
 emerging_lienage	GW.5
 emerging_lineage	JD.1
 emerging_lineage	XBB.1.41
+emerging_lineage	LB.1
+emerging_lineage	KP.2.3
+emerging_lineage	JN.1.50
+emerging_lineage	XDY
 
 ################
 
diff --git a/defaults/emerging_lineages.tsv b/defaults/emerging_lineages.tsv
index 31bcadb1c..01d7b4276 100644
--- a/defaults/emerging_lineages.tsv
+++ b/defaults/emerging_lineages.tsv
@@ -220,6 +220,19 @@ clade	gene	site	alt
 23I	nuc	15756	A
 23I	nuc	28958	A
 
+24A	clade	23I
+24A	nuc	11727	A
+24A	nuc	22926	C
+24A	nuc	27810	C
+
+24B	clade	24A
+24B	nuc	7113	T
+24B	nuc	17334	T
+24B	nuc	22928	C
+24B	nuc	24872	T
+
+24C	clade	24B
+24C	nuc	23039	G
 
 BA.2.3.20	clade	21L
 BA.2.3.20	nuc	6770	G
@@ -309,3 +322,22 @@ JD.1	nuc	22928	C
 XBB.1.41	clade	22F
 XBB.1.41	nuc	1473	T
 XBB.1.41	nuc	20102	T
+
+LB.1	clade	24A
+LB.1	nuc	22111	T
+LB.1	nuc	22928	C
+LB.1	nuc	22599	C
+
+KP.2.3	clade	24B
+KP.2.3	nuc	22599	C
+KP.2.3	nuc	25563	T
+
+JN.1.50	clade	24A
+JN.1.50	nuc	9298	T
+JN.1.50	nuc	22309	C
+JN.1.50	nuc	22930	G
+
+XDY	clade	24A
+XDY	nuc	19669	A
+XDY	nuc	22131	C
+XDY	nuc	23039	G