From 55c2587458faccca0fbb82398008d2e04c1d2bb1 Mon Sep 17 00:00:00 2001 From: Rachel Colquhoun Date: Wed, 16 Mar 2022 21:06:53 +0000 Subject: [PATCH 01/29] Add first draft for XE --- constellations/definitions/cXE.json | 62 +++++++++++++++++++++++++++++ 1 file changed, 62 insertions(+) create mode 100644 constellations/definitions/cXE.json diff --git a/constellations/definitions/cXE.json b/constellations/definitions/cXE.json new file mode 100644 index 0000000..89c933f --- /dev/null +++ b/constellations/definitions/cXE.json @@ -0,0 +1,62 @@ +{ + "label": "Omicron (XE-like)", + "description": "XE lineage defining mutations", + "sources": [ + ], + "type": "variant", + "variant": { + "Pango_lineages": [ + "XE" + ], + "WHO_label": "Omicron", + "mrca_lineage": "XE", + "lineage_name": "XE", + "parent_lineage": "B.1.1.529", + "representative_genome": "" + }, + "tags": [ + "XE", + "GL2" + ], + "sites": [ + "orf1ab:K856R", + "nuc:C3241T", + "nuc:T5386G", + "orf1ab:V1887I", + "del:6513:3", + "orf1ab:A2710T", + "nuc:C12880T", + "nuc:C14599T", + "nuc:C15714T", + "orf1ab:R5716C", + "orf1ab:T6564I", + "nuc:A20055G", + "spike:T19I", + "del:21633:9", + "nuc:T22200G", + "spike:S371F", + "spike:T376A", + "spike:D405N", + "spike:R408S", + "nuc:C25000T", + "nuc:C25584T", + "nuc:C26060T", + "nuc:C26858T", + "orf6:D61L", + "n:S413R" + ], + "note": "Unique mutations for sublineage", + "note2": "Requires ancestral mutation so scorpio tie breaks correctly", + "rules": { + "default": { + "min_alt": 17, + "max_ref": 3, + "nuc:C14599": "not ref" + }, + "Probable": { + "min_alt": 15, + "max_ref": 8, + "nuc:C14599": "not ref" + } + } +} From 6cc207866acf27b24e05d4e41ea5b3d5081edd58 Mon Sep 17 00:00:00 2001 From: Rachel Colquhoun Date: Thu, 17 Mar 2022 09:15:18 +0000 Subject: [PATCH 02/29] test no defining mutations in rules --- constellations/definitions/cBA.1.json | 6 ++---- constellations/definitions/cBA.2.json | 6 ++---- constellations/definitions/cBA.3.json | 8 ++------ constellations/definitions/cXE.json | 6 ++---- 4 files changed, 8 insertions(+), 18 deletions(-) diff --git a/constellations/definitions/cBA.1.json b/constellations/definitions/cBA.1.json index f627fa8..ec32931 100644 --- a/constellations/definitions/cBA.1.json +++ b/constellations/definitions/cBA.1.json @@ -47,13 +47,11 @@ "rules": { "default": { "min_alt": 14, - "max_ref": 3, - "nuc:T5386G": "not ref" + "max_ref": 3 }, "Probable": { "min_alt": 10, - "max_ref": 8, - "nuc:T5386G": "not ref" + "max_ref": 8 } } } diff --git a/constellations/definitions/cBA.2.json b/constellations/definitions/cBA.2.json index 5a24af3..800f855 100644 --- a/constellations/definitions/cBA.2.json +++ b/constellations/definitions/cBA.2.json @@ -52,13 +52,11 @@ "rules": { "default": { "min_alt": 18, - "max_ref": 3, - "orf1ab:R5716C": "not ref" + "max_ref": 3 }, "Probable": { "min_alt": 12, - "max_ref": 8, - "orf1ab:R5716C": "not ref" + "max_ref": 8 } } } diff --git a/constellations/definitions/cBA.3.json b/constellations/definitions/cBA.3.json index fd72dd6..d2074db 100644 --- a/constellations/definitions/cBA.3.json +++ b/constellations/definitions/cBA.3.json @@ -42,15 +42,11 @@ "rules": { "default": { "min_alt": 11, - "max_ref": 3, - "nuc:C832T": "not ref", - "nuc:C11235T": "not ref" + "max_ref": 3 }, "Probable": { "min_alt": 6, - "max_ref": 8, - "nuc:C832T": "not ref", - "nuc:C11235T": "not ref" + "max_ref": 8 } } } diff --git a/constellations/definitions/cXE.json b/constellations/definitions/cXE.json index 89c933f..d52a496 100644 --- a/constellations/definitions/cXE.json +++ b/constellations/definitions/cXE.json @@ -50,13 +50,11 @@ "rules": { "default": { "min_alt": 17, - "max_ref": 3, - "nuc:C14599": "not ref" + "max_ref": 3 }, "Probable": { "min_alt": 15, - "max_ref": 8, - "nuc:C14599": "not ref" + "max_ref": 8 } } } From 053c5ee819516e7e64405b19ca6e4bd55a894c55 Mon Sep 17 00:00:00 2001 From: Andrew Rambaut Date: Thu, 17 Mar 2022 11:43:46 +0000 Subject: [PATCH 03/29] Create cXAD.json --- constellations/definitions/cXAD.json | 81 ++++++++++++++++++++++++++++ 1 file changed, 81 insertions(+) create mode 100644 constellations/definitions/cXAD.json diff --git a/constellations/definitions/cXAD.json b/constellations/definitions/cXAD.json new file mode 100644 index 0000000..2b0be2d --- /dev/null +++ b/constellations/definitions/cXAD.json @@ -0,0 +1,81 @@ +{ + "label": "XD", + "description": "XD recombinant", + "sources": [ + ], + "type": "variant", + "variant": { + "Pango_lineages": [ + "XD" + ], + "mrca_lineage": "XD", + "lineage_name": "X", + "parent_lineage": "", + "incompatible_lineage_calls": [], + "representative_genome": "" + }, + "tags": [ + "XD" + ], + "sites": [ + "del:28271:1", + "del:22029:6", + "del:28248:6", + "orf1a:A1306S", + "orf1a:P2046L", + "orf1a:P2287S", + "orf1a:A2529V", + "nuc:C8986T", + "orf1a:V2930L", + "orf1a:T3255I", + "orf1a:T3646A", + "nuc:A11332G", + "orf1b:P314L", + "orf1b:G662S", + "orf1b:P1000L", + "orf1b:A1918V", + + "spike:S371L", + "spike:G142D", + "spike:G339D", + "spike:S373P", + "spike:S375F", + "spike:K417N", + "spike:N440K", + "spike:G446S", + "spike:S477N", + "spike:T478K", + "spike:E484A", + "spike:Q493R", + "spike:G496S", + "spike:Q498R", + "spike:N501Y", + "spike:Y505H", + "spike:T547K", + "spike:D614G", + "spike:H655Y", + "spike:N679K", + "spike:P681H", + "spike:N764K", + "spike:D796Y", + "spike:N856K", + "spike:Q954H", + "spike:N969K", + "spike:L981F", + + "ORF3a:S26L", + "M:I82T", + "ORF7a:V82A", + "ORF7a:T120I", + "N:D63G", + "N:R203M", + "n:G215C", + "N:D377Y" + "nuc:G29742T" + ], + "rules": { + "min_alt": 12, + "max_ref": 3, + "orf1a:A2529V": "alt" + } +} From 96737e1fdaebe37c1de2f9fb6d707086a7c06edf Mon Sep 17 00:00:00 2001 From: Andrew Rambaut Date: Thu, 17 Mar 2022 11:44:03 +0000 Subject: [PATCH 04/29] Rename cXAD.json to cXD.json --- constellations/definitions/{cXAD.json => cXD.json} | 0 1 file changed, 0 insertions(+), 0 deletions(-) rename constellations/definitions/{cXAD.json => cXD.json} (100%) diff --git a/constellations/definitions/cXAD.json b/constellations/definitions/cXD.json similarity index 100% rename from constellations/definitions/cXAD.json rename to constellations/definitions/cXD.json From 1aeedb47ef52e953777e044ac81f51d4e50af53c Mon Sep 17 00:00:00 2001 From: Andrew Rambaut Date: Thu, 17 Mar 2022 11:57:55 +0000 Subject: [PATCH 05/29] Update cXE.json --- constellations/definitions/cXE.json | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/constellations/definitions/cXE.json b/constellations/definitions/cXE.json index d52a496..51ed01a 100644 --- a/constellations/definitions/cXE.json +++ b/constellations/definitions/cXE.json @@ -9,9 +9,8 @@ "XE" ], "WHO_label": "Omicron", - "mrca_lineage": "XE", + "mrca_lineage": "XE", "lineage_name": "XE", - "parent_lineage": "B.1.1.529", "representative_genome": "" }, "tags": [ From 4a47515c81a1d717160b8856d6a7acd3699b46be Mon Sep 17 00:00:00 2001 From: Andrew Rambaut Date: Thu, 17 Mar 2022 15:32:34 +0000 Subject: [PATCH 06/29] Update cXD.json --- constellations/definitions/cXD.json | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/constellations/definitions/cXD.json b/constellations/definitions/cXD.json index 2b0be2d..fbe8a83 100644 --- a/constellations/definitions/cXD.json +++ b/constellations/definitions/cXD.json @@ -70,7 +70,7 @@ "N:D63G", "N:R203M", "n:G215C", - "N:D377Y" + "N:D377Y", "nuc:G29742T" ], "rules": { From 1e77ff8273948fd6da99cab749c4759276133c62 Mon Sep 17 00:00:00 2001 From: Andrew Rambaut Date: Fri, 18 Mar 2022 15:29:54 +0000 Subject: [PATCH 07/29] Create cXE-parent.json --- constellations/definitions/cXE-parent.json | 41 ++++++++++++++++++++++ 1 file changed, 41 insertions(+) create mode 100644 constellations/definitions/cXE-parent.json diff --git a/constellations/definitions/cXE-parent.json b/constellations/definitions/cXE-parent.json new file mode 100644 index 0000000..5033530 --- /dev/null +++ b/constellations/definitions/cXE-parent.json @@ -0,0 +1,41 @@ +{ + "label": "XE-parent1", + "description": "Majority parent of XE recombinant lineage", + "sources": [ + ], + "type": "variant", + "variant": { + "mrca_lineage": "", + "lineage_name": "XE-parent1", + "representative_genome": "" + }, + "tags": [ + "XE", + "GL2" + ], + "note": "Shared mutations for BA1 parent", + "note": "Likely breakpoint: between 10448 and 11287 (NSP5 or NSP6)", + "sites": [ + "nuc:C3037T", + "orf1ab:T3255I", + "orf1ab:P3395H", + "orf1ab:SGF3675-", + "orf1ab:P4715L", + "orf1ab:I5967V", + "orf1ab:K856R", + + "nuc:T5386G", + "del:6513:3", + "orf1ab:A2710T", + "orf1ab:L3674F", + "orf1ab:I3758V", + "nuc:T13195C", + "nuc:C15240T", + ], + "rules": { + "default": { + "min_alt": 12, + "max_ref": 2 + } + } +} From 10ad2dd0153124e12d24070132ba39a81d252efc Mon Sep 17 00:00:00 2001 From: Andrew Rambaut Date: Fri, 18 Mar 2022 15:31:59 +0000 Subject: [PATCH 08/29] Update cXE.json --- constellations/definitions/cXE.json | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/constellations/definitions/cXE.json b/constellations/definitions/cXE.json index 51ed01a..4094145 100644 --- a/constellations/definitions/cXE.json +++ b/constellations/definitions/cXE.json @@ -1,6 +1,6 @@ { "label": "Omicron (XE-like)", - "description": "XE lineage defining mutations", + "description": "XE recombinant lineage defining mutations", "sources": [ ], "type": "variant", @@ -9,6 +9,7 @@ "XE" ], "WHO_label": "Omicron", + "parent_lineage": "XE-parent1", "mrca_lineage": "XE", "lineage_name": "XE", "representative_genome": "" From 764bc462d58c11ac33de5924e468432b16c86214 Mon Sep 17 00:00:00 2001 From: Andrew Rambaut Date: Fri, 18 Mar 2022 15:41:05 +0000 Subject: [PATCH 09/29] Rename cXE-parent.json to cXE-parent1.json --- constellations/definitions/{cXE-parent.json => cXE-parent1.json} | 0 1 file changed, 0 insertions(+), 0 deletions(-) rename constellations/definitions/{cXE-parent.json => cXE-parent1.json} (100%) diff --git a/constellations/definitions/cXE-parent.json b/constellations/definitions/cXE-parent1.json similarity index 100% rename from constellations/definitions/cXE-parent.json rename to constellations/definitions/cXE-parent1.json From 0686582fba146ea83c819dd11340820aeecfb896 Mon Sep 17 00:00:00 2001 From: Andrew Rambaut Date: Fri, 18 Mar 2022 15:42:18 +0000 Subject: [PATCH 10/29] Create cXE-parent2.json --- constellations/definitions/cXE-parent2.json | 41 +++++++++++++++++++++ 1 file changed, 41 insertions(+) create mode 100644 constellations/definitions/cXE-parent2.json diff --git a/constellations/definitions/cXE-parent2.json b/constellations/definitions/cXE-parent2.json new file mode 100644 index 0000000..f025543 --- /dev/null +++ b/constellations/definitions/cXE-parent2.json @@ -0,0 +1,41 @@ +{ + "label": "XE-parent2", + "description": "3' parent of XE recombinant lineage", + "sources": [ + ], + "type": "variant", + "variant": { + "mrca_lineage": "", + "lineage_name": "XE-parent2", + "representative_genome": "" + }, + "tags": [ + "XE", + "GL2" + ], + "note": "Shared mutations for BA2 parent", + "note": "Likely breakpoint: between 10448 and 11287 (NSP5 or NSP6)", + "sites": [ + "nuc:C3037T", + "orf1ab:T3255I", + "orf1ab:P3395H", + "orf1ab:SGF3675-", + "orf1ab:P4715L", + "orf1ab:I5967V", + "orf1ab:K856R", + + "nuc:T5386G", + "del:6513:3", + "orf1ab:A2710T", + "orf1ab:L3674F", + "orf1ab:I3758V", + "nuc:T13195C", + "nuc:C15240T", + ], + "rules": { + "default": { + "min_alt": 12, + "max_ref": 2 + } + } +} From 1b6ae9e60319ce23853033a8c526a41ee6ff6a7f Mon Sep 17 00:00:00 2001 From: Andrew Rambaut Date: Fri, 18 Mar 2022 15:43:19 +0000 Subject: [PATCH 11/29] Update cXE.json --- constellations/definitions/cXE.json | 38 ++--------------------------- 1 file changed, 2 insertions(+), 36 deletions(-) diff --git a/constellations/definitions/cXE.json b/constellations/definitions/cXE.json index 4094145..9933620 100644 --- a/constellations/definitions/cXE.json +++ b/constellations/definitions/cXE.json @@ -9,7 +9,7 @@ "XE" ], "WHO_label": "Omicron", - "parent_lineage": "XE-parent1", + "parent_lineage": "XE-parent2", "mrca_lineage": "XE", "lineage_name": "XE", "representative_genome": "" @@ -18,43 +18,9 @@ "XE", "GL2" ], + "note": "Unique mutations for sublineage", "sites": [ - "orf1ab:K856R", - "nuc:C3241T", - "nuc:T5386G", - "orf1ab:V1887I", - "del:6513:3", - "orf1ab:A2710T", - "nuc:C12880T", - "nuc:C14599T", - "nuc:C15714T", - "orf1ab:R5716C", - "orf1ab:T6564I", - "nuc:A20055G", - "spike:T19I", - "del:21633:9", - "nuc:T22200G", - "spike:S371F", - "spike:T376A", - "spike:D405N", - "spike:R408S", - "nuc:C25000T", - "nuc:C25584T", - "nuc:C26060T", - "nuc:C26858T", - "orf6:D61L", - "n:S413R" ], - "note": "Unique mutations for sublineage", - "note2": "Requires ancestral mutation so scorpio tie breaks correctly", "rules": { - "default": { - "min_alt": 17, - "max_ref": 3 - }, - "Probable": { - "min_alt": 15, - "max_ref": 8 - } } } From bd405f2542593cff78ffb18065bb7c63da6bb5ba Mon Sep 17 00:00:00 2001 From: Andrew Rambaut Date: Fri, 18 Mar 2022 16:08:29 +0000 Subject: [PATCH 12/29] Update cXE-parent2.json --- constellations/definitions/cXE-parent2.json | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/constellations/definitions/cXE-parent2.json b/constellations/definitions/cXE-parent2.json index f025543..63013a1 100644 --- a/constellations/definitions/cXE-parent2.json +++ b/constellations/definitions/cXE-parent2.json @@ -5,8 +5,9 @@ ], "type": "variant", "variant": { - "mrca_lineage": "", + "mrca_lineage": "", "lineage_name": "XE-parent2", + "parent_lineage": "XE-parent1", "representative_genome": "" }, "tags": [ From f780586d57e942273284d66e69c43bb7a5b34709 Mon Sep 17 00:00:00 2001 From: Andrew Rambaut Date: Fri, 18 Mar 2022 16:21:03 +0000 Subject: [PATCH 13/29] Update cXE-parent1.json --- constellations/definitions/cXE-parent1.json | 18 ++++-------------- 1 file changed, 4 insertions(+), 14 deletions(-) diff --git a/constellations/definitions/cXE-parent1.json b/constellations/definitions/cXE-parent1.json index 5033530..7478c6e 100644 --- a/constellations/definitions/cXE-parent1.json +++ b/constellations/definitions/cXE-parent1.json @@ -5,8 +5,9 @@ ], "type": "variant", "variant": { - "mrca_lineage": "", + "mrca_lineage": "", "lineage_name": "XE-parent1", + "parent_lineage": "B.1.1.529", "representative_genome": "" }, "tags": [ @@ -16,26 +17,15 @@ "note": "Shared mutations for BA1 parent", "note": "Likely breakpoint: between 10448 and 11287 (NSP5 or NSP6)", "sites": [ - "nuc:C3037T", - "orf1ab:T3255I", - "orf1ab:P3395H", - "orf1ab:SGF3675-", - "orf1ab:P4715L", - "orf1ab:I5967V", "orf1ab:K856R", - "nuc:T5386G", "del:6513:3", "orf1ab:A2710T", - "orf1ab:L3674F", - "orf1ab:I3758V", - "nuc:T13195C", - "nuc:C15240T", ], "rules": { "default": { - "min_alt": 12, - "max_ref": 2 + "min_alt": 2, + "max_ref": 0 } } } From 1bea4105eb91c4e2281a206f861145794d72fba2 Mon Sep 17 00:00:00 2001 From: Andrew Rambaut Date: Fri, 18 Mar 2022 16:29:23 +0000 Subject: [PATCH 14/29] Update cXE-parent2.json --- constellations/definitions/cXE-parent2.json | 42 +++++++++++++-------- 1 file changed, 26 insertions(+), 16 deletions(-) diff --git a/constellations/definitions/cXE-parent2.json b/constellations/definitions/cXE-parent2.json index 63013a1..e6b10a9 100644 --- a/constellations/definitions/cXE-parent2.json +++ b/constellations/definitions/cXE-parent2.json @@ -17,26 +17,36 @@ "note": "Shared mutations for BA2 parent", "note": "Likely breakpoint: between 10448 and 11287 (NSP5 or NSP6)", "sites": [ - "nuc:C3037T", - "orf1ab:T3255I", - "orf1ab:P3395H", - "orf1ab:SGF3675-", - "orf1ab:P4715L", - "orf1ab:I5967V", - "orf1ab:K856R", - - "nuc:T5386G", - "del:6513:3", - "orf1ab:A2710T", - "orf1ab:L3674F", - "orf1ab:I3758V", - "nuc:T13195C", - "nuc:C15240T", + "orf1ab:L3027F", + "nuc:A9424G", + "orf1ab:T3090I", + "orf1ab:L3201F", + "nuc:C10198T", + "nuc:G10447A", + "nuc:C15714T", + "nuc:C12880T", + "nuc:C15714T", + "orf1ab:R5716C", + "orf1ab:T6564I", + "nuc:A20055G", + "spike:T19I", + "del:21633:9", + "nuc:T22200G", + "spike:S371F", + "spike:T376A", + "spike:D405N", + "spike:R408S", + "nuc:C25000T", + "nuc:C25584T", + "nuc:C26060T", + "nuc:C26858T", + "orf6:D61L", + "n:S413R" ], "rules": { "default": { "min_alt": 12, - "max_ref": 2 + "max_ref": 3 } } } From 899d0d48066b5f956954cf78099932b64497bfb9 Mon Sep 17 00:00:00 2001 From: Andrew Rambaut Date: Fri, 18 Mar 2022 16:30:50 +0000 Subject: [PATCH 15/29] Update cXE.json --- constellations/definitions/cXE.json | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/constellations/definitions/cXE.json b/constellations/definitions/cXE.json index 9933620..f980e35 100644 --- a/constellations/definitions/cXE.json +++ b/constellations/definitions/cXE.json @@ -18,9 +18,12 @@ "XE", "GL2" ], - "note": "Unique mutations for sublineage", + "note": "Unique mutations for XE sublineage", "sites": [ + "C14599T" ], "rules": { + "min_alt": 0, + "max_ref": 0 } } From 3366464b3890e61b169f8647fae96c0081cbdd4b Mon Sep 17 00:00:00 2001 From: Andrew Rambaut Date: Fri, 18 Mar 2022 17:23:39 +0000 Subject: [PATCH 16/29] Update cXE.json --- constellations/definitions/cXE.json | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/constellations/definitions/cXE.json b/constellations/definitions/cXE.json index f980e35..cda37c5 100644 --- a/constellations/definitions/cXE.json +++ b/constellations/definitions/cXE.json @@ -20,7 +20,7 @@ ], "note": "Unique mutations for XE sublineage", "sites": [ - "C14599T" + "nuc:C14599T" ], "rules": { "min_alt": 0, From 50f8e204ec39cccc45be3078dd6c032e3838bde7 Mon Sep 17 00:00:00 2001 From: Andrew Rambaut Date: Fri, 18 Mar 2022 17:28:10 +0000 Subject: [PATCH 17/29] Update cXE-parent1.json --- constellations/definitions/cXE-parent1.json | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/constellations/definitions/cXE-parent1.json b/constellations/definitions/cXE-parent1.json index 7478c6e..1d70dcb 100644 --- a/constellations/definitions/cXE-parent1.json +++ b/constellations/definitions/cXE-parent1.json @@ -20,7 +20,7 @@ "orf1ab:K856R", "nuc:T5386G", "del:6513:3", - "orf1ab:A2710T", + "orf1ab:A2710T" ], "rules": { "default": { From 58d280c6624589a40a96ba7634332fb555fbd8f7 Mon Sep 17 00:00:00 2001 From: Andrew Rambaut Date: Fri, 18 Mar 2022 18:08:30 +0000 Subject: [PATCH 18/29] Update cXE-parent2.json --- constellations/definitions/cXE-parent2.json | 8 +------- 1 file changed, 1 insertion(+), 7 deletions(-) diff --git a/constellations/definitions/cXE-parent2.json b/constellations/definitions/cXE-parent2.json index e6b10a9..bbb8f25 100644 --- a/constellations/definitions/cXE-parent2.json +++ b/constellations/definitions/cXE-parent2.json @@ -17,12 +17,6 @@ "note": "Shared mutations for BA2 parent", "note": "Likely breakpoint: between 10448 and 11287 (NSP5 or NSP6)", "sites": [ - "orf1ab:L3027F", - "nuc:A9424G", - "orf1ab:T3090I", - "orf1ab:L3201F", - "nuc:C10198T", - "nuc:G10447A", "nuc:C15714T", "nuc:C12880T", "nuc:C15714T", @@ -45,7 +39,7 @@ ], "rules": { "default": { - "min_alt": 12, + "min_alt": 11, "max_ref": 3 } } From 5bc286b5af885b0d0f550ffcdcecb0e78bde70b8 Mon Sep 17 00:00:00 2001 From: Andrew Rambaut Date: Wed, 6 Apr 2022 13:44:29 +0100 Subject: [PATCH 19/29] Create cBA.4.json Currently the same mutation list as BA.2. Need to make specific --- constellations/definitions/cBA.4.json | 62 +++++++++++++++++++++++++++ 1 file changed, 62 insertions(+) create mode 100644 constellations/definitions/cBA.4.json diff --git a/constellations/definitions/cBA.4.json b/constellations/definitions/cBA.4.json new file mode 100644 index 0000000..ed84c60 --- /dev/null +++ b/constellations/definitions/cBA.4.json @@ -0,0 +1,62 @@ +{ + "label": "Omicron (BA.4-like)", + "description": "BA.4 lineage defining mutations", + "sources": [ + ], + "type": "variant", + "variant": { + "Pango_lineages": [ + "BA.4" + ], + "WHO_label": "Omicron", + "mrca_lineage": "BA.4", + "lineage_name": "BA.4", + "parent_lineage": "B.1.1.529", + "representative_genome": "" + }, + "tags": [ + "BA.4" + ], + "sites": [ + "orf1ab:S135R", + "orf1ab:T842I", + "orf1ab:G1307S", + "nuc:C4321T", + "orf1ab:L3027F", + "nuc:A9424G", + "orf1ab:T3090I", + "orf1ab:L3201F", + "nuc:C10198T", + "nuc:G10447A", + "nuc:C15714T", + "nuc:C12880T", + "nuc:C15714T", + "orf1ab:R5716C", + "orf1ab:T6564I", + "nuc:A20055G", + "spike:T19I", + "del:21633:9", + "nuc:T22200G", + "spike:S371F", + "spike:T376A", + "spike:D405N", + "spike:R408S", + "nuc:C25000T", + "nuc:C25584T", + "nuc:C26060T", + "nuc:C26858T", + "orf6:D61L", + "n:S413R" + ], + "note": "Unique mutations for sublineage", + "rules": { + "default": { + "min_alt": 18, + "max_ref": 3 + }, + "Probable": { + "min_alt": 12, + "max_ref": 8 + } + } +} From ab15397f8ef393addaa51d4c8ba55e0cbe77f22e Mon Sep 17 00:00:00 2001 From: Andrew Rambaut Date: Wed, 6 Apr 2022 13:45:41 +0100 Subject: [PATCH 20/29] Create cBA.5.json Initial placeholder - mutation currently the same as BA.2 --- constellations/definitions/cBA.5.json | 62 +++++++++++++++++++++++++++ 1 file changed, 62 insertions(+) create mode 100644 constellations/definitions/cBA.5.json diff --git a/constellations/definitions/cBA.5.json b/constellations/definitions/cBA.5.json new file mode 100644 index 0000000..60a9461 --- /dev/null +++ b/constellations/definitions/cBA.5.json @@ -0,0 +1,62 @@ +{ + "label": "Omicron (BA.5-like)", + "description": "BA.5 lineage defining mutations", + "sources": [ + ], + "type": "variant", + "variant": { + "Pango_lineages": [ + "BA.5" + ], + "WHO_label": "Omicron", + "mrca_lineage": "BA.5", + "lineage_name": "BA.5", + "parent_lineage": "B.1.1.529", + "representative_genome": "" + }, + "tags": [ + "BA.5" + ], + "sites": [ + "orf1ab:S135R", + "orf1ab:T842I", + "orf1ab:G1307S", + "nuc:C4321T", + "orf1ab:L3027F", + "nuc:A9424G", + "orf1ab:T3090I", + "orf1ab:L3201F", + "nuc:C10198T", + "nuc:G10447A", + "nuc:C15714T", + "nuc:C12880T", + "nuc:C15714T", + "orf1ab:R5716C", + "orf1ab:T6564I", + "nuc:A20055G", + "spike:T19I", + "del:21633:9", + "nuc:T22200G", + "spike:S371F", + "spike:T376A", + "spike:D405N", + "spike:R408S", + "nuc:C25000T", + "nuc:C25584T", + "nuc:C26060T", + "nuc:C26858T", + "orf6:D61L", + "n:S413R" + ], + "note": "Unique mutations for sublineage", + "rules": { + "default": { + "min_alt": 18, + "max_ref": 3 + }, + "Probable": { + "min_alt": 12, + "max_ref": 8 + } + } +} From 33da43f422f127700380ecb301025ce92e4557a4 Mon Sep 17 00:00:00 2001 From: aineniamh Date: Fri, 8 Apr 2022 20:10:31 +0100 Subject: [PATCH 21/29] General notes: updating BA.4 and BA.5 constellations, moving mutations unique to BA.1, BA.2 and BA.3 from B.1.1.529 to each of their definitions. BA.5 has a reversion that must be ref in the definition. BA.4 has 12 mutations and BA.5 has 10 mutations that aren't in BA.2 (each share 26 and 24 mutations with BA.2 respectively) in these definition files. BA.5 and BA.4 share 9 mutations not present in BA.2 --- constellations/definitions/cB.1.1.529.json | 5 +- constellations/definitions/cBA.1.json | 5 +- constellations/definitions/cBA.2.json | 7 ++- constellations/definitions/cBA.3.json | 3 + constellations/definitions/cBA.4.json | 71 ++++++++++++---------- constellations/definitions/cBA.5.json | 66 ++++++++++---------- 6 files changed, 86 insertions(+), 71 deletions(-) diff --git a/constellations/definitions/cB.1.1.529.json b/constellations/definitions/cB.1.1.529.json index 9707512..84313c8 100644 --- a/constellations/definitions/cB.1.1.529.json +++ b/constellations/definitions/cB.1.1.529.json @@ -22,7 +22,6 @@ "nuc:C3037T", "orf1ab:T3255I", "orf1ab:P3395H", - "orf1ab:SGF3675-", "orf1ab:P4715L", "orf1ab:I5967V", "spike:G142D", @@ -34,7 +33,6 @@ "spike:S477N", "spike:T478K", "spike:E484A", - "spike:Q493R", "spike:Q498R", "spike:N501Y", "spike:Y505H", @@ -53,8 +51,7 @@ "nuc:C27807T", "nuc:A28271T", "n:P13L", - "del:28362:9", - "n:RG203KR" + "del:28362:9" ], "note": "Common mutations to the sublineages found", "rules": { diff --git a/constellations/definitions/cBA.1.json b/constellations/definitions/cBA.1.json index ec32931..9749688 100644 --- a/constellations/definitions/cBA.1.json +++ b/constellations/definitions/cBA.1.json @@ -23,6 +23,7 @@ "del:6513:3", "orf1ab:A2710T", "orf1ab:L3674F", + "orf1ab:SGF3675-", "orf1ab:I3758V", "nuc:T13195C", "nuc:C15240T", @@ -34,13 +35,15 @@ "nuc:22205+GAGCCAGAA", "spike:S371L", "spike:G446S", + "spike:Q493R", "spike:G496S", "spike:T547K", "spike:N856K", "spike:L981F", "nuc:C25000T", "nuc:C25584T", - "m:D3G" + "m:D3G", + "n:RG203KR" ], "note": "Unique mutations for sublineage", "note2": "Requires ancestral mutation so scorpio tie breaks correctly", diff --git a/constellations/definitions/cBA.2.json b/constellations/definitions/cBA.2.json index 800f855..ebd2396 100644 --- a/constellations/definitions/cBA.2.json +++ b/constellations/definitions/cBA.2.json @@ -26,6 +26,7 @@ "nuc:A9424G", "orf1ab:T3090I", "orf1ab:L3201F", + "orf1ab:SGF3675-", "nuc:C10198T", "nuc:G10447A", "nuc:C15714T", @@ -41,12 +42,14 @@ "spike:T376A", "spike:D405N", "spike:R408S", + "spike:Q493R", "nuc:C25000T", "nuc:C25584T", "nuc:C26060T", "nuc:C26858T", "orf6:D61L", - "n:S413R" + "n:RG203KR", + "n:S413R" ], "note": "Unique mutations for sublineage", "rules": { @@ -55,7 +58,7 @@ "max_ref": 3 }, "Probable": { - "min_alt": 12, + "min_alt": 15, "max_ref": 8 } } diff --git a/constellations/definitions/cBA.3.json b/constellations/definitions/cBA.3.json index d2074db..8949d6b 100644 --- a/constellations/definitions/cBA.3.json +++ b/constellations/definitions/cBA.3.json @@ -22,12 +22,14 @@ "nuc:C832T", "orf1ab:G1307S", "orf1ab:T3090I", + "orf1ab:SGF3675-", "nuc:G10447A", "nuc:C11235T", "nuc:C12880T", "nuc:C15714T", "orf1ab:I5967V", "spike:A67V", + "spike:Q493R", "del:21765:6", "del:21987:9", "del:22194:3", @@ -36,6 +38,7 @@ "spike:G446S", "orf3a:T223V", "nuc:C26858T", + "n:RG203KR", "n:S413R" ], "note": "Unique mutations for sublineage", diff --git a/constellations/definitions/cBA.4.json b/constellations/definitions/cBA.4.json index ed84c60..379de5d 100644 --- a/constellations/definitions/cBA.4.json +++ b/constellations/definitions/cBA.4.json @@ -18,44 +18,51 @@ "BA.4" ], "sites": [ - "orf1ab:S135R", - "orf1ab:T842I", - "orf1ab:G1307S", - "nuc:C4321T", - "orf1ab:L3027F", - "nuc:A9424G", - "orf1ab:T3090I", - "orf1ab:L3201F", - "nuc:C10198T", - "nuc:G10447A", - "nuc:C15714T", - "nuc:C12880T", - "nuc:C15714T", - "orf1ab:R5716C", - "orf1ab:T6564I", - "nuc:A20055G", - "spike:T19I", - "del:21633:9", - "nuc:T22200G", - "spike:S371F", - "spike:T376A", - "spike:D405N", - "spike:R408S", - "nuc:C25000T", - "nuc:C25584T", - "nuc:C26060T", - "nuc:C26858T", - "orf6:D61L", - "n:S413R" + "orf1ab:S135R", + "del:686:9", + "orf1ab:T842I", + "orf1ab:G1307S", + "nuc:C4321T", + "orf1ab:T3090I", + "nuc:C10198T", + "nuc:G10447A", + "del:11288:9", + "nuc:G12160A", + "nuc:C12880T", + "nuc:C15714T", + "orf1ab:R5716C", + "orf1ab:T6564I", + "nuc:A20055G", + "spike:T19I", + "del:21765:6", + "spike:V213G", + "spike:S371F", + "spike:T376A", + "spike:D405N", + "spike:L452R", + "spike:F486V", + "nuc:C25000T", + "orf3a:T223I", + "nuc:C26858T", + "orf6:D61L", + "nuc:G27788T", + "n:P151S", + "n:R203K", + "n:G204R", + "n:S413R", + "del:21633:9" ], "note": "Unique mutations for sublineage", "rules": { "default": { - "min_alt": 18, - "max_ref": 3 + "min_alt": 19, + "max_ref": 5, + "nsp4:L438":"ref", + "s:Q493":"ref", + "orf6:D61":"ref" }, "Probable": { - "min_alt": 12, + "min_alt": 17, "max_ref": 8 } } diff --git a/constellations/definitions/cBA.5.json b/constellations/definitions/cBA.5.json index 60a9461..2dc5a46 100644 --- a/constellations/definitions/cBA.5.json +++ b/constellations/definitions/cBA.5.json @@ -18,44 +18,46 @@ "BA.5" ], "sites": [ - "orf1ab:S135R", - "orf1ab:T842I", - "orf1ab:G1307S", - "nuc:C4321T", - "orf1ab:L3027F", - "nuc:A9424G", - "orf1ab:T3090I", - "orf1ab:L3201F", - "nuc:C10198T", - "nuc:G10447A", - "nuc:C15714T", - "nuc:C12880T", - "nuc:C15714T", - "orf1ab:R5716C", - "orf1ab:T6564I", - "nuc:A20055G", - "spike:T19I", - "del:21633:9", - "nuc:T22200G", - "spike:S371F", - "spike:T376A", - "spike:D405N", - "spike:R408S", - "nuc:C25000T", - "nuc:C25584T", - "nuc:C26060T", - "nuc:C26858T", - "orf6:D61L", - "n:S413R" + "orf1ab:S135R", + "orf1ab:T842I", + "orf1ab:G1307S", + "nuc:C4321T", + "orf1ab:T3090I", + "nuc:C10198T", + "nuc:G10447A", + "del:11288:9", + "nuc:G12160A", + "nuc:C12880T", + "nuc:C15714T", + "orf1ab:R5716C", + "orf1ab:T6564I", + "nuc:A20055G", + "spike:T19I", + "del:21633:9", + "del:21765:6", + "spike:V213G", + "spike:S371F", + "spike:T376A", + "spike:D405N", + "spike:L452R", + "spike:F486V", + "nuc:C25000T", + "nuc:C25584T", + "orf3a:T223I", + "m:D3N", + "n:R203K", + "n:G204R", + "n:S413R" ], "note": "Unique mutations for sublineage", "rules": { "default": { - "min_alt": 18, - "max_ref": 3 + "min_alt": 19, + "max_ref": 5, + "nuc:A27259C":"ref" }, "Probable": { - "min_alt": 12, + "min_alt": 17, "max_ref": 8 } } From 01d8391f8d4e96ee241097b6d756b064db427768 Mon Sep 17 00:00:00 2001 From: aineniamh Date: Fri, 8 Apr 2022 20:11:49 +0100 Subject: [PATCH 22/29] raising min alt threshold for ba.2, ba.4 and ba.5 --- constellations/definitions/cBA.2.json | 2 +- constellations/definitions/cBA.4.json | 2 +- constellations/definitions/cBA.5.json | 2 +- 3 files changed, 3 insertions(+), 3 deletions(-) diff --git a/constellations/definitions/cBA.2.json b/constellations/definitions/cBA.2.json index ebd2396..2671cd8 100644 --- a/constellations/definitions/cBA.2.json +++ b/constellations/definitions/cBA.2.json @@ -54,7 +54,7 @@ "note": "Unique mutations for sublineage", "rules": { "default": { - "min_alt": 18, + "min_alt": 20, "max_ref": 3 }, "Probable": { diff --git a/constellations/definitions/cBA.4.json b/constellations/definitions/cBA.4.json index 379de5d..f77bbc6 100644 --- a/constellations/definitions/cBA.4.json +++ b/constellations/definitions/cBA.4.json @@ -55,7 +55,7 @@ "note": "Unique mutations for sublineage", "rules": { "default": { - "min_alt": 19, + "min_alt": 24, "max_ref": 5, "nsp4:L438":"ref", "s:Q493":"ref", diff --git a/constellations/definitions/cBA.5.json b/constellations/definitions/cBA.5.json index 2dc5a46..083de46 100644 --- a/constellations/definitions/cBA.5.json +++ b/constellations/definitions/cBA.5.json @@ -52,7 +52,7 @@ "note": "Unique mutations for sublineage", "rules": { "default": { - "min_alt": 19, + "min_alt": 24, "max_ref": 5, "nuc:A27259C":"ref" }, From 73761e118a90b5c1cbd1ecce3a91246592382065 Mon Sep 17 00:00:00 2001 From: aineniamh Date: Fri, 8 Apr 2022 20:27:46 +0100 Subject: [PATCH 23/29] update v number --- constellations/__init__.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/constellations/__init__.py b/constellations/__init__.py index df7d7b0..a6c8c24 100644 --- a/constellations/__init__.py +++ b/constellations/__init__.py @@ -1,3 +1,3 @@ _program = "constellations" -__version__ = "v0.1.4" +__version__ = "v0.1.5" From 67ccd00ee2484f6ecfe2397df3ea4f861ebc0814 Mon Sep 17 00:00:00 2001 From: aineniamh Date: Fri, 8 Apr 2022 20:56:00 +0100 Subject: [PATCH 24/29] playing around with rules- haven't solved misassignment of South_Africa/NCV1010/2022 yet --- constellations/definitions/cBA.4.json | 7 +++++-- constellations/definitions/cBA.5.json | 9 +++++++-- 2 files changed, 12 insertions(+), 4 deletions(-) diff --git a/constellations/definitions/cBA.4.json b/constellations/definitions/cBA.4.json index f77bbc6..4ee81a8 100644 --- a/constellations/definitions/cBA.4.json +++ b/constellations/definitions/cBA.4.json @@ -55,11 +55,14 @@ "note": "Unique mutations for sublineage", "rules": { "default": { - "min_alt": 24, + "min_alt": 28, "max_ref": 5, + "m:D3N":"ref", + "nuc:C25584T":"ref", "nsp4:L438":"ref", "s:Q493":"ref", - "orf6:D61":"ref" + "orf6:D61":"alt", + "n:P151S":"alt" }, "Probable": { "min_alt": 17, diff --git a/constellations/definitions/cBA.5.json b/constellations/definitions/cBA.5.json index 083de46..798c100 100644 --- a/constellations/definitions/cBA.5.json +++ b/constellations/definitions/cBA.5.json @@ -52,9 +52,14 @@ "note": "Unique mutations for sublineage", "rules": { "default": { - "min_alt": 24, + "min_alt": 28, "max_ref": 5, - "nuc:A27259C":"ref" + "nuc:C26858T":"ref", + "nuc:A27259C":"ref", + "nuc:G27788T":"ref", + "n:P151S":"ref", + "m:D3N":"alt", + "nuc:C25584T":"alt" }, "Probable": { "min_alt": 17, From 328a51f5d6f2d97f5ed01f9f6b89b78a9e927999 Mon Sep 17 00:00:00 2001 From: aineniamh Date: Sat, 9 Apr 2022 11:32:38 +0100 Subject: [PATCH 25/29] modifying ba.4 and ba.5 (and adding rules to ba.2) after manual curation of alignment of designated seqeunces --- constellations/definitions/cBA.2.json | 8 +++++--- constellations/definitions/cBA.4.json | 19 ++++++++----------- constellations/definitions/cBA.5.json | 21 ++++++++++----------- 3 files changed, 23 insertions(+), 25 deletions(-) diff --git a/constellations/definitions/cBA.2.json b/constellations/definitions/cBA.2.json index 2671cd8..727b444 100644 --- a/constellations/definitions/cBA.2.json +++ b/constellations/definitions/cBA.2.json @@ -54,11 +54,13 @@ "note": "Unique mutations for sublineage", "rules": { "default": { - "min_alt": 20, - "max_ref": 3 + "min_alt": 28, + "max_ref": 3, + "spike:Q493":"alt", + "nuc:G27788":"ref" }, "Probable": { - "min_alt": 15, + "min_alt": 20, "max_ref": 8 } } diff --git a/constellations/definitions/cBA.4.json b/constellations/definitions/cBA.4.json index 4ee81a8..36bcd49 100644 --- a/constellations/definitions/cBA.4.json +++ b/constellations/definitions/cBA.4.json @@ -19,7 +19,6 @@ ], "sites": [ "orf1ab:S135R", - "del:686:9", "orf1ab:T842I", "orf1ab:G1307S", "nuc:C4321T", @@ -34,7 +33,8 @@ "orf1ab:T6564I", "nuc:A20055G", "spike:T19I", - "del:21765:6", + "s:HV69-", + "nuc:T22200G", "spike:V213G", "spike:S371F", "spike:T376A", @@ -42,30 +42,27 @@ "spike:L452R", "spike:F486V", "nuc:C25000T", - "orf3a:T223I", + "nuc:C25584T", + "nuc:C26060T", "nuc:C26858T", "orf6:D61L", "nuc:G27788T", "n:P151S", - "n:R203K", - "n:G204R", - "n:S413R", - "del:21633:9" + "n:RG203KR", + "n:S413R" ], "note": "Unique mutations for sublineage", "rules": { "default": { - "min_alt": 28, + "min_alt": 30, "max_ref": 5, "m:D3N":"ref", - "nuc:C25584T":"ref", - "nsp4:L438":"ref", "s:Q493":"ref", "orf6:D61":"alt", "n:P151S":"alt" }, "Probable": { - "min_alt": 17, + "min_alt": 20, "max_ref": 8 } } diff --git a/constellations/definitions/cBA.5.json b/constellations/definitions/cBA.5.json index 798c100..0a80b6b 100644 --- a/constellations/definitions/cBA.5.json +++ b/constellations/definitions/cBA.5.json @@ -33,8 +33,8 @@ "orf1ab:T6564I", "nuc:A20055G", "spike:T19I", - "del:21633:9", - "del:21765:6", + "s:HV69-", + "nuc:T22200G", "spike:V213G", "spike:S371F", "spike:T376A", @@ -43,10 +43,9 @@ "spike:F486V", "nuc:C25000T", "nuc:C25584T", - "orf3a:T223I", + "nuc:C26060T", "m:D3N", - "n:R203K", - "n:G204R", + "n:RG203KR", "n:S413R" ], "note": "Unique mutations for sublineage", @@ -54,15 +53,15 @@ "default": { "min_alt": 28, "max_ref": 5, - "nuc:C26858T":"ref", - "nuc:A27259C":"ref", - "nuc:G27788T":"ref", - "n:P151S":"ref", - "m:D3N":"alt", + "nuc:C26858":"ref", + "nuc:A27259":"ref", + "nuc:G27788":"ref", + "n:P151":"ref", + "m:D3":"alt", "nuc:C25584T":"alt" }, "Probable": { - "min_alt": 17, + "min_alt": 20, "max_ref": 8 } } From be122438752a4ca1c4ca4f9c18f5d2f0b64d9711 Mon Sep 17 00:00:00 2001 From: aineniamh Date: Sat, 9 Apr 2022 11:55:09 +0100 Subject: [PATCH 26/29] updating rules for 2 and 5 --- constellations/definitions/cBA.2.json | 1 + constellations/definitions/cBA.5.json | 5 ++--- 2 files changed, 3 insertions(+), 3 deletions(-) diff --git a/constellations/definitions/cBA.2.json b/constellations/definitions/cBA.2.json index 727b444..41d4ef2 100644 --- a/constellations/definitions/cBA.2.json +++ b/constellations/definitions/cBA.2.json @@ -57,6 +57,7 @@ "min_alt": 28, "max_ref": 3, "spike:Q493":"alt", + "n:P151":"ref", "nuc:G27788":"ref" }, "Probable": { diff --git a/constellations/definitions/cBA.5.json b/constellations/definitions/cBA.5.json index 0a80b6b..d68f452 100644 --- a/constellations/definitions/cBA.5.json +++ b/constellations/definitions/cBA.5.json @@ -53,12 +53,11 @@ "default": { "min_alt": 28, "max_ref": 5, + "s:Q493":"ref", "nuc:C26858":"ref", - "nuc:A27259":"ref", "nuc:G27788":"ref", "n:P151":"ref", - "m:D3":"alt", - "nuc:C25584T":"alt" + "m:D3":"alt" }, "Probable": { "min_alt": 20, From bfd3b0fedc2d80df7cc6340d460b8eb4005864d8 Mon Sep 17 00:00:00 2001 From: aineniamh Date: Tue, 12 Apr 2022 08:57:28 +0100 Subject: [PATCH 27/29] D61 to not ref --- constellations/definitions/cBA.4.json | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/constellations/definitions/cBA.4.json b/constellations/definitions/cBA.4.json index 36bcd49..25effd2 100644 --- a/constellations/definitions/cBA.4.json +++ b/constellations/definitions/cBA.4.json @@ -58,7 +58,7 @@ "max_ref": 5, "m:D3N":"ref", "s:Q493":"ref", - "orf6:D61":"alt", + "orf6:D61":"not ref", "n:P151S":"alt" }, "Probable": { From 652e8d0742f6f426eff9be1898b89641dd414564 Mon Sep 17 00:00:00 2001 From: aineniamh Date: Tue, 12 Apr 2022 10:36:16 +0100 Subject: [PATCH 28/29] rm XE for now --- constellations/definitions/cXE-parent1.json | 31 -------------- constellations/definitions/cXE-parent2.json | 46 --------------------- constellations/definitions/cXE.json | 29 ------------- 3 files changed, 106 deletions(-) delete mode 100644 constellations/definitions/cXE-parent1.json delete mode 100644 constellations/definitions/cXE-parent2.json delete mode 100644 constellations/definitions/cXE.json diff --git a/constellations/definitions/cXE-parent1.json b/constellations/definitions/cXE-parent1.json deleted file mode 100644 index 1d70dcb..0000000 --- a/constellations/definitions/cXE-parent1.json +++ /dev/null @@ -1,31 +0,0 @@ -{ - "label": "XE-parent1", - "description": "Majority parent of XE recombinant lineage", - "sources": [ - ], - "type": "variant", - "variant": { - "mrca_lineage": "", - "lineage_name": "XE-parent1", - "parent_lineage": "B.1.1.529", - "representative_genome": "" - }, - "tags": [ - "XE", - "GL2" - ], - "note": "Shared mutations for BA1 parent", - "note": "Likely breakpoint: between 10448 and 11287 (NSP5 or NSP6)", - "sites": [ - "orf1ab:K856R", - "nuc:T5386G", - "del:6513:3", - "orf1ab:A2710T" - ], - "rules": { - "default": { - "min_alt": 2, - "max_ref": 0 - } - } -} diff --git a/constellations/definitions/cXE-parent2.json b/constellations/definitions/cXE-parent2.json deleted file mode 100644 index bbb8f25..0000000 --- a/constellations/definitions/cXE-parent2.json +++ /dev/null @@ -1,46 +0,0 @@ -{ - "label": "XE-parent2", - "description": "3' parent of XE recombinant lineage", - "sources": [ - ], - "type": "variant", - "variant": { - "mrca_lineage": "", - "lineage_name": "XE-parent2", - "parent_lineage": "XE-parent1", - "representative_genome": "" - }, - "tags": [ - "XE", - "GL2" - ], - "note": "Shared mutations for BA2 parent", - "note": "Likely breakpoint: between 10448 and 11287 (NSP5 or NSP6)", - "sites": [ - "nuc:C15714T", - "nuc:C12880T", - "nuc:C15714T", - "orf1ab:R5716C", - "orf1ab:T6564I", - "nuc:A20055G", - "spike:T19I", - "del:21633:9", - "nuc:T22200G", - "spike:S371F", - "spike:T376A", - "spike:D405N", - "spike:R408S", - "nuc:C25000T", - "nuc:C25584T", - "nuc:C26060T", - "nuc:C26858T", - "orf6:D61L", - "n:S413R" - ], - "rules": { - "default": { - "min_alt": 11, - "max_ref": 3 - } - } -} diff --git a/constellations/definitions/cXE.json b/constellations/definitions/cXE.json deleted file mode 100644 index cda37c5..0000000 --- a/constellations/definitions/cXE.json +++ /dev/null @@ -1,29 +0,0 @@ -{ - "label": "Omicron (XE-like)", - "description": "XE recombinant lineage defining mutations", - "sources": [ - ], - "type": "variant", - "variant": { - "Pango_lineages": [ - "XE" - ], - "WHO_label": "Omicron", - "parent_lineage": "XE-parent2", - "mrca_lineage": "XE", - "lineage_name": "XE", - "representative_genome": "" - }, - "tags": [ - "XE", - "GL2" - ], - "note": "Unique mutations for XE sublineage", - "sites": [ - "nuc:C14599T" - ], - "rules": { - "min_alt": 0, - "max_ref": 0 - } -} From 586a2353696bdb6d36ec24883dc2cc879275a43d Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?=C3=81ine=20O=27Toole?= Date: Tue, 12 Apr 2022 10:53:38 +0100 Subject: [PATCH 29/29] Delete cXD.json --- constellations/definitions/cXD.json | 81 ----------------------------- 1 file changed, 81 deletions(-) delete mode 100644 constellations/definitions/cXD.json diff --git a/constellations/definitions/cXD.json b/constellations/definitions/cXD.json deleted file mode 100644 index fbe8a83..0000000 --- a/constellations/definitions/cXD.json +++ /dev/null @@ -1,81 +0,0 @@ -{ - "label": "XD", - "description": "XD recombinant", - "sources": [ - ], - "type": "variant", - "variant": { - "Pango_lineages": [ - "XD" - ], - "mrca_lineage": "XD", - "lineage_name": "X", - "parent_lineage": "", - "incompatible_lineage_calls": [], - "representative_genome": "" - }, - "tags": [ - "XD" - ], - "sites": [ - "del:28271:1", - "del:22029:6", - "del:28248:6", - "orf1a:A1306S", - "orf1a:P2046L", - "orf1a:P2287S", - "orf1a:A2529V", - "nuc:C8986T", - "orf1a:V2930L", - "orf1a:T3255I", - "orf1a:T3646A", - "nuc:A11332G", - "orf1b:P314L", - "orf1b:G662S", - "orf1b:P1000L", - "orf1b:A1918V", - - "spike:S371L", - "spike:G142D", - "spike:G339D", - "spike:S373P", - "spike:S375F", - "spike:K417N", - "spike:N440K", - "spike:G446S", - "spike:S477N", - "spike:T478K", - "spike:E484A", - "spike:Q493R", - "spike:G496S", - "spike:Q498R", - "spike:N501Y", - "spike:Y505H", - "spike:T547K", - "spike:D614G", - "spike:H655Y", - "spike:N679K", - "spike:P681H", - "spike:N764K", - "spike:D796Y", - "spike:N856K", - "spike:Q954H", - "spike:N969K", - "spike:L981F", - - "ORF3a:S26L", - "M:I82T", - "ORF7a:V82A", - "ORF7a:T120I", - "N:D63G", - "N:R203M", - "n:G215C", - "N:D377Y", - "nuc:G29742T" - ], - "rules": { - "min_alt": 12, - "max_ref": 3, - "orf1a:A2529V": "alt" - } -}