From 5c838b1bf9f21e3cb18a5fcf4ca29c7e3c84f02f Mon Sep 17 00:00:00 2001 From: Trevor Bedford Date: Wed, 25 Sep 2024 13:18:14 -0700 Subject: [PATCH 1/2] Elevate lineage XEC as clade 24F This commit elevates Pango lineage XEC as clade 24F --- defaults/clade_display_names.yml | 1 + defaults/clade_emergence_dates.tsv | 3 ++- defaults/clade_hierarchy.tsv | 1 + defaults/clades.tsv | 4 ++++ defaults/color_ordering.tsv | 1 + 5 files changed, 9 insertions(+), 1 deletion(-) diff --git a/defaults/clade_display_names.yml b/defaults/clade_display_names.yml index 8806974a7..26c79ec7d 100644 --- a/defaults/clade_display_names.yml +++ b/defaults/clade_display_names.yml @@ -43,3 +43,4 @@ 24C: 24C (KP.3) 24D: 24D (XDV.1) 24E: 24E (KP.3.1.1) +24F: 24F (XEC) diff --git a/defaults/clade_emergence_dates.tsv b/defaults/clade_emergence_dates.tsv index d55128dcf..efb1a44ee 100644 --- a/defaults/clade_emergence_dates.tsv +++ b/defaults/clade_emergence_dates.tsv @@ -44,4 +44,5 @@ 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 2024-06-01 diff --git a/defaults/clade_hierarchy.tsv b/defaults/clade_hierarchy.tsv index 3b36a11f4..a52af6ad5 100644 --- a/defaults/clade_hierarchy.tsv +++ b/defaults/clade_hierarchy.tsv @@ -43,3 +43,4 @@ clade parent WHO 24C 24B Omicron 24D 21L Omicron 24E 24C Omicron +24F 24C Omicron diff --git a/defaults/clades.tsv b/defaults/clades.tsv index 31a32b40f..68b54b367 100644 --- a/defaults/clades.tsv +++ b/defaults/clades.tsv @@ -244,3 +244,7 @@ clade gene site alt 24E nuc 13121 T 24E nuc 15372 T 24E nuc 19722 G + +24F clade 24C +24F nuc 2060 A + diff --git a/defaults/color_ordering.tsv b/defaults/color_ordering.tsv index 5c11dd2bf..897b2bbe4 100644 --- a/defaults/color_ordering.tsv +++ b/defaults/color_ordering.tsv @@ -34043,6 +34043,7 @@ 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) ################ From 811906bf665a0cdaf1bf23533a39b74b31839cb6 Mon Sep 17 00:00:00 2001 From: Cornelius Roemer Date: Thu, 3 Oct 2024 16:32:20 +0200 Subject: [PATCH 2/2] Add 24G (KP.2.3) --- defaults/clade_display_names.yml | 1 + defaults/clade_emergence_dates.tsv | 3 ++- defaults/clade_hierarchy.tsv | 3 ++- defaults/clades.tsv | 15 ++++++++++++--- defaults/color_ordering.tsv | 2 +- defaults/emerging_lineages.tsv | 4 ---- 6 files changed, 18 insertions(+), 10 deletions(-) diff --git a/defaults/clade_display_names.yml b/defaults/clade_display_names.yml index 26c79ec7d..fbfa1ae7d 100644 --- a/defaults/clade_display_names.yml +++ b/defaults/clade_display_names.yml @@ -44,3 +44,4 @@ 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 efb1a44ee..5b23745c6 100644 --- a/defaults/clade_emergence_dates.tsv +++ b/defaults/clade_emergence_dates.tsv @@ -45,4 +45,5 @@ Nextstrain_clade first_sequence 24C 2023-12-01 24D 2024-01-01 24E 2023-12-01 -24F 2024-06-01 +24F 2024-05-01 +24G 2024-01-01 diff --git a/defaults/clade_hierarchy.tsv b/defaults/clade_hierarchy.tsv index a52af6ad5..b782d1b8c 100644 --- a/defaults/clade_hierarchy.tsv +++ b/defaults/clade_hierarchy.tsv @@ -43,4 +43,5 @@ clade parent WHO 24C 24B Omicron 24D 21L Omicron 24E 24C Omicron -24F 24C Omicron +24F 24A Omicron +24G 24B Omicron diff --git a/defaults/clades.tsv b/defaults/clades.tsv index 68b54b367..0d87646b4 100644 --- a/defaults/clades.tsv +++ b/defaults/clades.tsv @@ -245,6 +245,15 @@ clade gene site alt 24E nuc 15372 T 24E nuc 19722 G -24F clade 24C -24F nuc 2060 A - +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 897b2bbe4..d90c42f7c 100644 --- a/defaults/color_ordering.tsv +++ b/defaults/color_ordering.tsv @@ -34044,6 +34044,7 @@ 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) ################ @@ -34065,7 +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