From ca0478e252a560f4fc59974a3a4bc0dd6bc37e21 Mon Sep 17 00:00:00 2001 From: Cornelius Roemer Date: Fri, 20 Dec 2024 03:47:25 +0100 Subject: [PATCH 1/2] Designate LP.8.1 as clade 24J --- defaults/clade_display_names.yml | 1 + defaults/clade_emergence_dates.tsv | 1 + defaults/clade_hierarchy.tsv | 1 + defaults/clades.tsv | 6 ++++++ defaults/color_ordering.tsv | 1 + 5 files changed, 10 insertions(+) diff --git a/defaults/clade_display_names.yml b/defaults/clade_display_names.yml index ac05d0e29..ee35e9433 100644 --- a/defaults/clade_display_names.yml +++ b/defaults/clade_display_names.yml @@ -47,3 +47,4 @@ 24G: 24G (KP.2.3) 24H: 24H (LF.7) 24I: 24I (MV.1) +24J: 24J (LP.8.1) diff --git a/defaults/clade_emergence_dates.tsv b/defaults/clade_emergence_dates.tsv index 773e35d79..4f85afd54 100644 --- a/defaults/clade_emergence_dates.tsv +++ b/defaults/clade_emergence_dates.tsv @@ -49,3 +49,4 @@ Nextstrain_clade first_sequence 24G 2024-01-01 24H 2024-05-01 24I 2024-05-01 +24J 2024-07-01 diff --git a/defaults/clade_hierarchy.tsv b/defaults/clade_hierarchy.tsv index dc4e52c6d..b5119a81e 100644 --- a/defaults/clade_hierarchy.tsv +++ b/defaults/clade_hierarchy.tsv @@ -47,3 +47,4 @@ clade parent WHO 24G 24B Omicron 24H 24A Omicron 24I 24A Omicron +24J 24B Omicron diff --git a/defaults/clades.tsv b/defaults/clades.tsv index c519d3acb..ce5f0053a 100644 --- a/defaults/clades.tsv +++ b/defaults/clades.tsv @@ -266,3 +266,9 @@ clade gene site alt 24I nuc 936 T 24I nuc 7393 T 24I nuc 22995 C + +24J clade 24B +24J nuc 4999 T +24J nuc 22110 A +24J nuc 22132 T +24J nuc 25925 T \ No newline at end of file diff --git a/defaults/color_ordering.tsv b/defaults/color_ordering.tsv index d62d46433..cc432baaa 100644 --- a/defaults/color_ordering.tsv +++ b/defaults/color_ordering.tsv @@ -34047,6 +34047,7 @@ clade_membership 24F (XEC) clade_membership 24G (KP.2.3) clade_membership 24H (LF.7) clade_membership 24I (MV.1) +clade_membership 24J (LP.8.1) ################ From c6a88b6438f326230413d2e8fcb9aaeabcd0626a Mon Sep 17 00:00:00 2001 From: Trevor Bedford Date: Thu, 23 Jan 2025 16:47:28 -0800 Subject: [PATCH 2/2] Update name of LP.8.1 to clade 25A --- defaults/clade_display_names.yml | 2 +- defaults/clade_emergence_dates.tsv | 2 +- defaults/clade_hierarchy.tsv | 2 +- defaults/clades.tsv | 10 +++++----- defaults/color_ordering.tsv | 2 +- 5 files changed, 9 insertions(+), 9 deletions(-) diff --git a/defaults/clade_display_names.yml b/defaults/clade_display_names.yml index ee35e9433..d43ec7643 100644 --- a/defaults/clade_display_names.yml +++ b/defaults/clade_display_names.yml @@ -47,4 +47,4 @@ 24G: 24G (KP.2.3) 24H: 24H (LF.7) 24I: 24I (MV.1) -24J: 24J (LP.8.1) +25A: 25A (LP.8.1) diff --git a/defaults/clade_emergence_dates.tsv b/defaults/clade_emergence_dates.tsv index 4f85afd54..317fb8a47 100644 --- a/defaults/clade_emergence_dates.tsv +++ b/defaults/clade_emergence_dates.tsv @@ -49,4 +49,4 @@ Nextstrain_clade first_sequence 24G 2024-01-01 24H 2024-05-01 24I 2024-05-01 -24J 2024-07-01 +25A 2024-07-01 diff --git a/defaults/clade_hierarchy.tsv b/defaults/clade_hierarchy.tsv index b5119a81e..52b0ce59c 100644 --- a/defaults/clade_hierarchy.tsv +++ b/defaults/clade_hierarchy.tsv @@ -47,4 +47,4 @@ clade parent WHO 24G 24B Omicron 24H 24A Omicron 24I 24A Omicron -24J 24B Omicron +25A 24B Omicron diff --git a/defaults/clades.tsv b/defaults/clades.tsv index ce5f0053a..38244d053 100644 --- a/defaults/clades.tsv +++ b/defaults/clades.tsv @@ -267,8 +267,8 @@ clade gene site alt 24I nuc 7393 T 24I nuc 22995 C -24J clade 24B -24J nuc 4999 T -24J nuc 22110 A -24J nuc 22132 T -24J nuc 25925 T \ No newline at end of file +25A clade 24B +25A nuc 4999 T +25A nuc 22110 A +25A nuc 22132 T +25A nuc 25925 T diff --git a/defaults/color_ordering.tsv b/defaults/color_ordering.tsv index cc432baaa..ef743926b 100644 --- a/defaults/color_ordering.tsv +++ b/defaults/color_ordering.tsv @@ -34047,7 +34047,7 @@ clade_membership 24F (XEC) clade_membership 24G (KP.2.3) clade_membership 24H (LF.7) clade_membership 24I (MV.1) -clade_membership 24J (LP.8.1) +clade_membership 25A (LP.8.1) ################