From 69345ba9ae30aa279cc1e65167f6e8fbcd391cf8 Mon Sep 17 00:00:00 2001 From: Cornelius Roemer Date: Mon, 31 Jul 2023 15:15:26 +0200 Subject: [PATCH 1/3] Add five new clades --- defaults/clade_display_names.yml | 5 +++ defaults/clade_emergence_dates.tsv | 7 ++- defaults/clade_hierarchy.tsv | 5 +++ defaults/clades.tsv | 33 +++++++++++++- defaults/color_ordering.tsv | 11 +++-- defaults/emerging_lineages.tsv | 69 ++++++++++++++---------------- 6 files changed, 85 insertions(+), 45 deletions(-) diff --git a/defaults/clade_display_names.yml b/defaults/clade_display_names.yml index c9ccc649e..dc1355346 100644 --- a/defaults/clade_display_names.yml +++ b/defaults/clade_display_names.yml @@ -31,3 +31,8 @@ 22F: 22F (XBB) 23A: 23A (XBB.1.5) 23B: 23B (XBB.1.16) +23C: 23C (XBC) +23D: 23D (CH.1.1) +23E: 23E (XBB.1.9) +23F: 23F (XBB.2.3) +23G: 23G (EG.5) diff --git a/defaults/clade_emergence_dates.tsv b/defaults/clade_emergence_dates.tsv index 16682b8a3..18ffce777 100644 --- a/defaults/clade_emergence_dates.tsv +++ b/defaults/clade_emergence_dates.tsv @@ -30,6 +30,11 @@ Nextstrain_clade first_sequence 22C 2021-12-01 22D 2022-04-01 22E 2022-07-10 -22F 2022-08-01 +22F 2022-07-01 23A 2022-10-01 23B 2022-11-01 +23C 2022-07-01 +23D 2022-06-01 +23E 2022-08-01 +23F 2022-10-01 +23G 2022-12-01 diff --git a/defaults/clade_hierarchy.tsv b/defaults/clade_hierarchy.tsv index 02c00aecc..10f5e27c2 100644 --- a/defaults/clade_hierarchy.tsv +++ b/defaults/clade_hierarchy.tsv @@ -31,3 +31,8 @@ clade parent WHO 22F 21L Omicron 23A 22F Omicron 23B 22F Omicron +23C 20A Delta/Omicron +23D 22D Omicron +23E 22F Omicron +23F 22F Omicron +23G 23E Omicron diff --git a/defaults/clades.tsv b/defaults/clades.tsv index 3ccfd68e1..7a6b8e447 100644 --- a/defaults/clades.tsv +++ b/defaults/clades.tsv @@ -179,4 +179,35 @@ clade gene site alt 23B nuc 12730 A 23B nuc 14856 G 23B nuc 18703 T -23B nuc 28447 G \ No newline at end of file +23B nuc 28447 G + +23C clade 20A +23C nuc 7091 A +23C nuc 21635 T +23C nuc 23670 T +23C nuc 27898 C +23C nuc 27718 C + +23D clade 22D +23D nuc 3857 A +23D nuc 20741 G +23D nuc 22599 C +23D nuc 22917 G +23D nuc 22893 C +23D nuc 23019 C + +23E clade 22F +23E nuc 5720 A +23E nuc 12789 T +23E nuc 28297 C + +23F clade 22F +23F nuc 4234 T +23F nuc 23123 T +23F nuc 27431 T + +23G clade 23E +23G nuc 2334 T +23G nuc 9693 T +23G nuc 22480 T +23G nuc 22930 A diff --git a/defaults/color_ordering.tsv b/defaults/color_ordering.tsv index b2244e86e..5997f8dc0 100644 --- a/defaults/color_ordering.tsv +++ b/defaults/color_ordering.tsv @@ -34031,25 +34031,24 @@ clade_membership 22E (BQ.1) clade_membership 22F (XBB) clade_membership 23A (XBB.1.5) clade_membership 23B (XBB.1.16) +clade_membership 23C (XBC) +clade_membership 23D (CH.1.1) +clade_membership 23E (XBB.1.9) +clade_membership 23F (XBB.2.3) +clade_membership 23G (EG.5) ################ emerging_lineage BA.2.3.20 emerging_lineage BN.1 -emerging_lineage CH.1.1 emerging_lineage XAY -emerging_lineage XBC -emerging_lineage XBB.1.9 emerging_lineage XBB.1.9.1 -emerging_lineage XBB.1.9.2 -emerging_lineage EG.5 emerging_lineage XBB.1.42 emerging_lineage XBB.1.22.1 emerging_lineage XBB.1.19 emerging_lineage XBB.1.17.1 emerging_lineage FE.1 -emerging_lineage XBB.2.3 ################ diff --git a/defaults/emerging_lineages.tsv b/defaults/emerging_lineages.tsv index d10b40f13..2e8ea69a6 100644 --- a/defaults/emerging_lineages.tsv +++ b/defaults/emerging_lineages.tsv @@ -181,6 +181,37 @@ clade gene site alt 23B nuc 18703 T 23B nuc 28447 G +23C clade 20A +23C nuc 7091 A +23C nuc 21635 T +23C nuc 23670 T +23C nuc 27898 C +23C nuc 27718 C + +23D clade 22D +23D nuc 3857 A +23D nuc 20741 G +23D nuc 22599 C +23D nuc 22917 G +23D nuc 22893 C +23D nuc 23019 C + +23E clade 22F +23E nuc 5720 A +23E nuc 12789 T +23E nuc 28297 C + +23F clade 22F +23F nuc 4234 T +23F nuc 23123 T +23F nuc 27431 T + +23G clade 23E +23G nuc 2334 T +23G nuc 9693 T +23G nuc 22480 T +23G nuc 22930 A + BA.2.3.20 clade 21L BA.2.3.20 nuc 6770 G BA.2.3.20 nuc 22332 A @@ -192,13 +223,6 @@ BN.1 nuc 22599 C BN.1 nuc 22629 C BN.1 nuc 23031 C -XBC clade 20A -XBC nuc 23670 T -XBC nuc 27898 C -XBC nuc 21635 T -XBC nuc 27718 C -XBC nuc 7091 A - XAY clade 20A XAY nuc 12163 A XAY nuc 21618 G @@ -207,38 +231,15 @@ XAY nuc 22899 A XAY nuc 23679 T XAY nuc 27575 G -CH.1.1 clade 22D -CH.1.1 nuc 3857 A -CH.1.1 nuc 23019 C -CH.1.1 nuc 22599 C -CH.1.1 nuc 20741 G -CH.1.1 nuc 22893 C -CH.1.1 nuc 22917 G - FE.1 clade 22F FE.1 nuc 3662 G FE.1 nuc 8001 G FE.1 nuc 26012 G -XBB.1.9 clade 22F -XBB.1.9 nuc 5720 A -XBB.1.9 nuc 12789 T -XBB.1.9 nuc 28297 C - -XBB.1.9.1 clade XBB.1.9 +XBB.1.9.1 clade 23E XBB.1.9.1 nuc 11956 T XBB.1.9.1 nuc 23018 C -XBB.1.9.2 clade XBB.1.9 -XBB.1.9.2 nuc 16878 T -XBB.1.9.2 nuc 23018 C -XBB.1.9.2 nuc 27507 C - -XBB.2.3 clade 22F -XBB.2.3 nuc 4234 T -XBB.2.3 nuc 23123 T -XBB.2.3 nuc 27431 T - XBB.1.22.1 clade 22F XBB.1.22.1 nuc 22161 G XBB.1.22.1 nuc 23018 C @@ -262,9 +263,3 @@ XBB.1.19 nuc 10042 G XBB.1.19 nuc 21363 T XBB.1.19 nuc 23018 C XBB.1.19 nuc 27915 G - -EG.5 clade XBB.1.9.2 -EG.5 nuc 2334 T -EG.5 nuc 9693 T -EG.5 nuc 22480 T -EG.5 nuc 22930 A \ No newline at end of file From f745a10a2e8ba041352eeac9aced6ae5a5357ee9 Mon Sep 17 00:00:00 2001 From: Cornelius Roemer Date: Mon, 7 Aug 2023 17:26:59 +0200 Subject: [PATCH 2/3] Remove XBC from list of new clades --- defaults/clade_display_names.yml | 9 +++-- defaults/clade_emergence_dates.tsv | 9 +++-- defaults/clade_hierarchy.tsv | 7 ++-- defaults/clades.tsv | 49 +++++++++++--------------- defaults/color_ordering.tsv | 10 +++--- defaults/emerging_lineages.tsv | 56 ++++++++++++++++-------------- 6 files changed, 66 insertions(+), 74 deletions(-) diff --git a/defaults/clade_display_names.yml b/defaults/clade_display_names.yml index dc1355346..54cccf7fb 100644 --- a/defaults/clade_display_names.yml +++ b/defaults/clade_display_names.yml @@ -31,8 +31,7 @@ 22F: 22F (XBB) 23A: 23A (XBB.1.5) 23B: 23B (XBB.1.16) -23C: 23C (XBC) -23D: 23D (CH.1.1) -23E: 23E (XBB.1.9) -23F: 23F (XBB.2.3) -23G: 23G (EG.5) +23C: 23C (CH.1.1) +23D: 23D (XBB.1.9) +23E: 23E (XBB.2.3) +23F: 23F (EG.5.1) diff --git a/defaults/clade_emergence_dates.tsv b/defaults/clade_emergence_dates.tsv index 18ffce777..c01fcebc6 100644 --- a/defaults/clade_emergence_dates.tsv +++ b/defaults/clade_emergence_dates.tsv @@ -33,8 +33,7 @@ Nextstrain_clade first_sequence 22F 2022-07-01 23A 2022-10-01 23B 2022-11-01 -23C 2022-07-01 -23D 2022-06-01 -23E 2022-08-01 -23F 2022-10-01 -23G 2022-12-01 +23C 2022-06-01 +23D 2022-08-01 +23E 2022-10-01 +23F 2023-01-01 diff --git a/defaults/clade_hierarchy.tsv b/defaults/clade_hierarchy.tsv index 10f5e27c2..20a3824c5 100644 --- a/defaults/clade_hierarchy.tsv +++ b/defaults/clade_hierarchy.tsv @@ -31,8 +31,7 @@ clade parent WHO 22F 21L Omicron 23A 22F Omicron 23B 22F Omicron -23C 20A Delta/Omicron -23D 22D Omicron +23C 22D Omicron +23D 22F Omicron 23E 22F Omicron -23F 22F Omicron -23G 23E Omicron +23F 23D Omicron diff --git a/defaults/clades.tsv b/defaults/clades.tsv index 7a6b8e447..41ec7b7f8 100644 --- a/defaults/clades.tsv +++ b/defaults/clades.tsv @@ -181,33 +181,26 @@ clade gene site alt 23B nuc 18703 T 23B nuc 28447 G -23C clade 20A -23C nuc 7091 A -23C nuc 21635 T -23C nuc 23670 T -23C nuc 27898 C -23C nuc 27718 C - -23D clade 22D -23D nuc 3857 A -23D nuc 20741 G -23D nuc 22599 C -23D nuc 22917 G -23D nuc 22893 C -23D nuc 23019 C +23C clade 22D +23C nuc 3857 A +23C nuc 20741 G +23C nuc 22599 C +23C nuc 22917 G +23C nuc 22893 C +23C nuc 23019 C + +23D clade 22F +23D nuc 5720 A +23D nuc 12789 T +23D nuc 28297 C 23E clade 22F -23E nuc 5720 A -23E nuc 12789 T -23E nuc 28297 C - -23F clade 22F -23F nuc 4234 T -23F nuc 23123 T -23F nuc 27431 T - -23G clade 23E -23G nuc 2334 T -23G nuc 9693 T -23G nuc 22480 T -23G nuc 22930 A +23E nuc 4234 T +23E nuc 23123 T +23E nuc 27431 T + +23F clade 23D +23F nuc 2334 T +23F nuc 9693 T +23F nuc 22480 T +23F nuc 22930 A diff --git a/defaults/color_ordering.tsv b/defaults/color_ordering.tsv index 5997f8dc0..20efc2a0d 100644 --- a/defaults/color_ordering.tsv +++ b/defaults/color_ordering.tsv @@ -34031,11 +34031,10 @@ clade_membership 22E (BQ.1) clade_membership 22F (XBB) clade_membership 23A (XBB.1.5) clade_membership 23B (XBB.1.16) -clade_membership 23C (XBC) -clade_membership 23D (CH.1.1) -clade_membership 23E (XBB.1.9) -clade_membership 23F (XBB.2.3) -clade_membership 23G (EG.5) +clade_membership 23C (CH.1.1) +clade_membership 23D (XBB.1.9) +clade_membership 23E (XBB.2.3) +clade_membership 23F (EG.5.1) ################ @@ -34043,6 +34042,7 @@ clade_membership 23G (EG.5) emerging_lineage BA.2.3.20 emerging_lineage BN.1 emerging_lineage XAY +emerging_lineage XBC emerging_lineage XBB.1.9.1 emerging_lineage XBB.1.42 emerging_lineage XBB.1.22.1 diff --git a/defaults/emerging_lineages.tsv b/defaults/emerging_lineages.tsv index 2e8ea69a6..15c92310e 100644 --- a/defaults/emerging_lineages.tsv +++ b/defaults/emerging_lineages.tsv @@ -181,36 +181,31 @@ clade gene site alt 23B nuc 18703 T 23B nuc 28447 G -23C clade 20A -23C nuc 7091 A -23C nuc 21635 T -23C nuc 23670 T -23C nuc 27898 C -23C nuc 27718 C - -23D clade 22D -23D nuc 3857 A -23D nuc 20741 G -23D nuc 22599 C -23D nuc 22917 G -23D nuc 22893 C -23D nuc 23019 C + +23C clade 22D +23C nuc 3857 A +23C nuc 20741 G +23C nuc 22599 C +23C nuc 22917 G +23C nuc 22893 C +23C nuc 23019 C + +23D clade 22F +23D nuc 5720 A +23D nuc 12789 T +23D nuc 28297 C 23E clade 22F -23E nuc 5720 A -23E nuc 12789 T -23E nuc 28297 C +23E nuc 4234 T +23E nuc 23123 T +23E nuc 27431 T -23F clade 22F -23F nuc 4234 T -23F nuc 23123 T -23F nuc 27431 T +23F clade 23D +23F nuc 2334 T +23F nuc 9693 T +23F nuc 22480 T +23F nuc 22930 A -23G clade 23E -23G nuc 2334 T -23G nuc 9693 T -23G nuc 22480 T -23G nuc 22930 A BA.2.3.20 clade 21L BA.2.3.20 nuc 6770 G @@ -223,6 +218,13 @@ BN.1 nuc 22599 C BN.1 nuc 22629 C BN.1 nuc 23031 C +XBC clade 20A +XBC nuc 23670 T +XBC nuc 27898 C +XBC nuc 21635 T +XBC nuc 27718 C +XBC nuc 7091 A + XAY clade 20A XAY nuc 12163 A XAY nuc 21618 G @@ -236,7 +238,7 @@ FE.1 nuc 3662 G FE.1 nuc 8001 G FE.1 nuc 26012 G -XBB.1.9.1 clade 23E +XBB.1.9.1 clade 23D XBB.1.9.1 nuc 11956 T XBB.1.9.1 nuc 23018 C From 168c6c01bd75f7e020a0a6a87fe3c3baa34e9fe6 Mon Sep 17 00:00:00 2001 From: Cornelius Roemer Date: Mon, 7 Aug 2023 19:00:46 +0200 Subject: [PATCH 3/3] Add 52H as required mutation for 23F (EG.5.1) --- defaults/clades.tsv | 1 + 1 file changed, 1 insertion(+) diff --git a/defaults/clades.tsv b/defaults/clades.tsv index 41ec7b7f8..b76078e8a 100644 --- a/defaults/clades.tsv +++ b/defaults/clades.tsv @@ -202,5 +202,6 @@ clade gene site alt 23F clade 23D 23F nuc 2334 T 23F nuc 9693 T +23F nuc 21718 T 23F nuc 22480 T 23F nuc 22930 A