From 6434f5da97982e34ce9f2df9890a891eddaa30c7 Mon Sep 17 00:00:00 2001 From: Trevor Bedford Date: Fri, 4 Oct 2024 05:05:29 -0700 Subject: [PATCH] Elevate lineage XEC as clade 24F and KP.2.3 as clade 23G (#1152) * Elevate lineage XEC as clade 24F This commit elevates Pango lineage XEC as clade 24F * Add 24G (KP.2.3) --------- Co-authored-by: Cornelius Roemer --- defaults/clade_display_names.yml | 2 ++ defaults/clade_emergence_dates.tsv | 4 +++- defaults/clade_hierarchy.tsv | 2 ++ defaults/clades.tsv | 13 +++++++++++++ defaults/color_ordering.tsv | 3 ++- defaults/emerging_lineages.tsv | 4 ---- 6 files changed, 22 insertions(+), 6 deletions(-) diff --git a/defaults/clade_display_names.yml b/defaults/clade_display_names.yml index 8806974a7..fbfa1ae7d 100644 --- a/defaults/clade_display_names.yml +++ b/defaults/clade_display_names.yml @@ -43,3 +43,5 @@ 24C: 24C (KP.3) 24D: 24D (XDV.1) 24E: 24E (KP.3.1.1) +24F: 24F (XEC) +24G: 24G (KP.2.3) diff --git a/defaults/clade_emergence_dates.tsv b/defaults/clade_emergence_dates.tsv index d55128dcf..5b23745c6 100644 --- a/defaults/clade_emergence_dates.tsv +++ b/defaults/clade_emergence_dates.tsv @@ -44,4 +44,6 @@ Nextstrain_clade first_sequence 24B 2023-11-01 24C 2023-12-01 24D 2024-01-01 -24E 2023-12-01 \ No newline at end of file +24E 2023-12-01 +24F 2024-05-01 +24G 2024-01-01 diff --git a/defaults/clade_hierarchy.tsv b/defaults/clade_hierarchy.tsv index 3b36a11f4..b782d1b8c 100644 --- a/defaults/clade_hierarchy.tsv +++ b/defaults/clade_hierarchy.tsv @@ -43,3 +43,5 @@ clade parent WHO 24C 24B Omicron 24D 21L Omicron 24E 24C Omicron +24F 24A Omicron +24G 24B Omicron diff --git a/defaults/clades.tsv b/defaults/clades.tsv index 31a32b40f..0d87646b4 100644 --- a/defaults/clades.tsv +++ b/defaults/clades.tsv @@ -244,3 +244,16 @@ clade gene site alt 24E nuc 13121 T 24E nuc 15372 T 24E nuc 19722 G + +24F clade 24A +24F nuc 18657 T +24F nuc 19716 T +24F nuc 21627 A +24F nuc 21738 C +24F nuc 22928 C +24F nuc 23039 G +24F nuc 24872 T + +24G clade 24B +24G nuc 22599 C +24G nuc 25593 T diff --git a/defaults/color_ordering.tsv b/defaults/color_ordering.tsv index 5c11dd2bf..d90c42f7c 100644 --- a/defaults/color_ordering.tsv +++ b/defaults/color_ordering.tsv @@ -34043,6 +34043,8 @@ clade_membership 24B (JN.1.11.1) clade_membership 24C (KP.3) clade_membership 24D (XDV.1) clade_membership 24E (KP.3.1.1) +clade_membership 24F (XEC) +clade_membership 24G (KP.2.3) ################ @@ -34064,7 +34066,6 @@ 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 01d7b4276..fe5657e2a 100644 --- a/defaults/emerging_lineages.tsv +++ b/defaults/emerging_lineages.tsv @@ -328,10 +328,6 @@ 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