From b2bda2d8967e8716cf4caf6e2737779050c76b58 Mon Sep 17 00:00:00 2001 From: Cornelius Roemer Date: Wed, 29 Nov 2023 14:01:59 +0100 Subject: [PATCH 1/2] Designate clades 23G (XBB.1.5.70), 23H (HK.3), 23I (BA.2.86) Add emerging lineages JD.1 (XBB.1.5.102.1), XBB.1.41, JN.1 (BA.2.86.1) --- defaults/clade_display_names.yml | 3 +++ defaults/clade_emergence_dates.tsv | 3 +++ defaults/clade_hierarchy.tsv | 3 +++ defaults/clades.tsv | 14 +++++++++++ defaults/color_ordering.tsv | 9 ++++--- defaults/emerging_lineages.tsv | 40 +++++++++++++++++++----------- 6 files changed, 55 insertions(+), 17 deletions(-) diff --git a/defaults/clade_display_names.yml b/defaults/clade_display_names.yml index 54cccf7fb..b99b72236 100644 --- a/defaults/clade_display_names.yml +++ b/defaults/clade_display_names.yml @@ -35,3 +35,6 @@ 23D: 23D (XBB.1.9) 23E: 23E (XBB.2.3) 23F: 23F (EG.5.1) +23G: 23G (XBB.1.5.70) +23H: 23H (HK.3) +23I: 23I (BA.2.86) diff --git a/defaults/clade_emergence_dates.tsv b/defaults/clade_emergence_dates.tsv index c01fcebc6..428d4d244 100644 --- a/defaults/clade_emergence_dates.tsv +++ b/defaults/clade_emergence_dates.tsv @@ -37,3 +37,6 @@ Nextstrain_clade first_sequence 23D 2022-08-01 23E 2022-10-01 23F 2023-01-01 +23G 2023-01-01 +23H 2023-03-01 +23I 2023-04-01 diff --git a/defaults/clade_hierarchy.tsv b/defaults/clade_hierarchy.tsv index 20a3824c5..5b3dcbbf8 100644 --- a/defaults/clade_hierarchy.tsv +++ b/defaults/clade_hierarchy.tsv @@ -35,3 +35,6 @@ clade parent WHO 23D 22F Omicron 23E 22F Omicron 23F 23D Omicron +23G 23A Omicron +23H 23F Omicron +23I 21L Omicron diff --git a/defaults/clades.tsv b/defaults/clades.tsv index b76078e8a..4a60262e4 100644 --- a/defaults/clades.tsv +++ b/defaults/clades.tsv @@ -205,3 +205,17 @@ clade gene site alt 23F nuc 21718 T 23F nuc 22480 T 23F nuc 22930 A + +23G clade 23A +23G nuc 8737 C +23G nuc 25045 G +23G nuc 28005 T + +23H clade 23F +23H nuc 13627 A +23H nuc 22927 T + +23I clade 21L +23I nuc 897 A +23I nuc 15756 A +23I nuc 28958 A diff --git a/defaults/color_ordering.tsv b/defaults/color_ordering.tsv index 02ab6ee1e..95964fbf3 100644 --- a/defaults/color_ordering.tsv +++ b/defaults/color_ordering.tsv @@ -34035,6 +34035,9 @@ clade_membership 23C (CH.1.1) clade_membership 23D (XBB.1.9) clade_membership 23E (XBB.2.3) clade_membership 23F (EG.5.1) +clade_membership 23G (XBB.1.5.70 +clade_membership 23H (HK.3) +clade_membership 23I (BA.2.86) ################ @@ -34049,13 +34052,13 @@ emerging_lineage XBB.1.22.1 emerging_lineage XBB.1.17.1 emerging_lineage FE.1 emerging_lineage FL.1.5.1 -emerging_lineage XBB.1.5.70 emerging_lineage XBB.1.16.6 emerging_lineage DV.7.1 emerging_lineage HV.1 -emerging_lineage HK.3 -emerging_lineage BA.2.86 emerging_lienage GW.5 +emerging_lineage JD.1 +emerging_lineage XBB.1.41 +emerging_lineage JN.1 ################ diff --git a/defaults/emerging_lineages.tsv b/defaults/emerging_lineages.tsv index bbd241bf0..405a82260 100644 --- a/defaults/emerging_lineages.tsv +++ b/defaults/emerging_lineages.tsv @@ -206,6 +206,20 @@ clade gene site alt 23F nuc 22480 T 23F nuc 22930 A +23G clade 23A +23G nuc 8737 C +23G nuc 25045 G +23G nuc 28005 T + +23H clade 23F +23H nuc 13627 A +23H nuc 22927 T + +23I clade 21L +23I nuc 897 A +23I nuc 15756 A +23I nuc 28958 A + BA.2.3.20 clade 21L BA.2.3.20 nuc 6770 G @@ -265,11 +279,6 @@ FL.1.5.1 nuc 3242 A FL.1.5.1 nuc 20060 T FL.1.5.1 nuc 22995 G -XBB.1.5.70 clade 23A -XBB.1.5.70 nuc 8737 C -XBB.1.5.70 nuc 25045 G -XBB.1.5.70 nuc 28005 T - XBB.1.16.6 clade 23B XBB.1.16.6 nuc 12397 G XBB.1.16.6 nuc 8947 T @@ -285,15 +294,6 @@ HV.1 nuc 5835 T HV.1 nuc 22033 A HV.1 nuc 22917 G -HK.3 clade 23F -HK.3 nuc 13627 A -HK.3 nuc 22927 T - -BA.2.86 clade 21L -BA.2.86 nuc 15756 A -BA.2.86 nuc 897 A -BA.2.86 nuc 28958 A - GW.5 clade 22F GW.5 nuc 1170 T GW.5 nuc 6501 A @@ -301,3 +301,15 @@ GW.5 nuc 10042 G GW.5 nuc 21363 T GW.5 nuc 27915 G +JD.1 clade 23A +JD.1 nuc 14634 G +JD.1 nuc 22927 T +JD.1 nuc 22928 C + +XBB.1.41 clade 22F +XBB.1.41 nuc 1473 T +XBB.1.41 nuc 20102 T + +JN.1 clade 23I +JN.1 nuc 11727 A +JN.1 nuc 22926 C From 094cf7c679fbfbd13e54a19fd5476f9eeb05f1d6 Mon Sep 17 00:00:00 2001 From: Cornelius Roemer Date: Wed, 29 Nov 2023 18:21:57 +0100 Subject: [PATCH 2/2] fix: missing closing paren in color ordering --- defaults/color_ordering.tsv | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/defaults/color_ordering.tsv b/defaults/color_ordering.tsv index 95964fbf3..d39be3931 100644 --- a/defaults/color_ordering.tsv +++ b/defaults/color_ordering.tsv @@ -34035,7 +34035,7 @@ clade_membership 23C (CH.1.1) clade_membership 23D (XBB.1.9) clade_membership 23E (XBB.2.3) clade_membership 23F (EG.5.1) -clade_membership 23G (XBB.1.5.70 +clade_membership 23G (XBB.1.5.70) clade_membership 23H (HK.3) clade_membership 23I (BA.2.86)