From a804602e259a91a6afda5455e96982b7a98b0d3b Mon Sep 17 00:00:00 2001 From: Rachel Colquhoun Date: Tue, 23 May 2023 14:38:23 +0100 Subject: [PATCH] add some xbb --- constellations/definitions/cB.1.1.529.json | 1 - constellations/definitions/cBA.2.json | 7 ++-- constellations/definitions/cXBB-parent1.json | 31 +++++++++++++++ constellations/definitions/cXBB-parent2.json | 27 +++++++++++++ constellations/definitions/cXBB.1.16.json | 32 +++++++++++++++ constellations/definitions/cXBB.1.5.json | 31 +++++++++++++++ constellations/definitions/cXBB.1.json | 30 ++++++++++++++ constellations/definitions/cXBB.json | 41 ++++++++++++++++++++ 8 files changed, 195 insertions(+), 5 deletions(-) create mode 100644 constellations/definitions/cXBB-parent1.json create mode 100644 constellations/definitions/cXBB-parent2.json create mode 100644 constellations/definitions/cXBB.1.16.json create mode 100644 constellations/definitions/cXBB.1.5.json create mode 100644 constellations/definitions/cXBB.1.json create mode 100644 constellations/definitions/cXBB.json diff --git a/constellations/definitions/cB.1.1.529.json b/constellations/definitions/cB.1.1.529.json index 60a4f6d..76f0a37 100644 --- a/constellations/definitions/cB.1.1.529.json +++ b/constellations/definitions/cB.1.1.529.json @@ -28,7 +28,6 @@ "spike:G339D", "spike:S373P", "spike:S375F", - "spike:K417N", "spike:N440K", "spike:S477N", "spike:T478K", diff --git a/constellations/definitions/cBA.2.json b/constellations/definitions/cBA.2.json index 3d6c051..4a4f61d 100644 --- a/constellations/definitions/cBA.2.json +++ b/constellations/definitions/cBA.2.json @@ -21,7 +21,7 @@ ], "sites": [ "orf1ab:S135R", - "orf1ab:T842I", + "orf1ab:T842I", "orf1ab:G1307S", "nuc:C4321T", "orf1ab:L3027F", @@ -38,15 +38,14 @@ "nuc:A20055G", "spike:T19I", "del:21633:9", - "nuc:T22200G", + "spike:V213G", "spike:S371F", "spike:T376A", "spike:D405N", - "spike:R408S", "spike:Q493R", + "orf3a:T223I", "nuc:C25000T", "nuc:C25584T", - "nuc:C26060T", "nuc:C26858T", "orf6:D61L", "n:RG203KR", diff --git a/constellations/definitions/cXBB-parent1.json b/constellations/definitions/cXBB-parent1.json new file mode 100644 index 0000000..0fe8848 --- /dev/null +++ b/constellations/definitions/cXBB-parent1.json @@ -0,0 +1,31 @@ +{ + "label": "XBB-parent1", + "description": "Majority parent of XBB recombinant lineage", + "sources": [ + ], + "type": "variant", + "variant": { + "mrca_lineage": "", + "lineage_name": "XBB-parent1", + "parent_lineage": "BA.2", + "representative_genome": "" + }, + "tags": [ + "XBB" + ], + "note": "Shared mutations with BA.2.75 parent", + "note": "Likely breakpoint: ~ S:446", + "sites": [ + "spike:G339H", + "spike:G446S", + "spike:N460K", + "e:T11A", + "nuc:C25416T" + ], + "rules": { + "default": { + "min_alt": 2, + "max_ref": 0 + } + } +} diff --git a/constellations/definitions/cXBB-parent2.json b/constellations/definitions/cXBB-parent2.json new file mode 100644 index 0000000..fefa8fc --- /dev/null +++ b/constellations/definitions/cXBB-parent2.json @@ -0,0 +1,27 @@ +{ + "label": "XBB-parent2", + "description": "Minority parent of XBB recombinant lineage", + "sources": [ + ], + "type": "variant", + "variant": { + "mrca_lineage": "", + "lineage_name": "XBB-parent2", + "parent_lineage": "XBB-parent1", + "representative_genome": "" + }, + "tags": [ + "XBB" + ], + "note": "Shared mutations with BA.2.10.1 parent", + "note": "Likely breakpoint: ~ S:446", + "sites": [ + "orf1b:S959P" + ], + "rules": { + "default": { + "min_alt": 0, + "max_ref": 0 + } + } +} diff --git a/constellations/definitions/cXBB.1.16.json b/constellations/definitions/cXBB.1.16.json new file mode 100644 index 0000000..9840907 --- /dev/null +++ b/constellations/definitions/cXBB.1.16.json @@ -0,0 +1,32 @@ +{ + "label": "Omicron (XBB.1.16-like)", + "description": "XBB.1.16 lineage defining mutations", + "sources": [ + ], + "type": "variant", + "variant": { + "Pango_lineages": [ + "XBB.1.16" + ], + "WHO_label": "Omicron", + "parent_lineage": "XBB.1", + "mrca_lineage": "XBB.1.16", + "lineage_name": "XBB.1.16", + "representative_genome": "" + }, + "tags": [ + "XBB.1.16" + ], + "note": "Unique mutations for XBB.1.16 sublineage", + "sites": [ + "orf1b:D1746Y", + "spike:E180V", + "nuc:T28297C", + "nuc:A28447G", + "nuc:C29386T" + ], + "rules": { + "min_alt": 3, + "max_ref": 1 + } +} diff --git a/constellations/definitions/cXBB.1.5.json b/constellations/definitions/cXBB.1.5.json new file mode 100644 index 0000000..0ece676 --- /dev/null +++ b/constellations/definitions/cXBB.1.5.json @@ -0,0 +1,31 @@ +{ + "label": "Omicron (XBB.1.5-like)", + "description": "XBB.1.5 lineage defining mutations", + "sources": [ + ], + "type": "variant", + "variant": { + "Pango_lineages": [ + "XBB.1.5" + ], + "WHO_label": "Omicron", + "parent_lineage": "XBB.1", + "mrca_lineage": "XBB.1.5", + "lineage_name": "XBB.1.5", + "representative_genome": "" + }, + "tags": [ + "XBB.1.5" + ], + "note": "Unique mutations for XBB.1.5 sublineage", + "sites": [ + "nuc:T17124C", + "spike:G252V", + "spike:F486P" + ], + "rules": { + "min_alt": 1, + "max_ref": 1, + "spike:F486":"alt" + } +} diff --git a/constellations/definitions/cXBB.1.json b/constellations/definitions/cXBB.1.json new file mode 100644 index 0000000..070c5e0 --- /dev/null +++ b/constellations/definitions/cXBB.1.json @@ -0,0 +1,30 @@ +{ + "label": "Omicron (XBB.1-like)", + "description": "XBB.1 lineage defining mutations", + "sources": [ + ], + "type": "variant", + "variant": { + "Pango_lineages": [ + "XBB.1" + ], + "WHO_label": "Omicron", + "parent_lineage": "XBB", + "mrca_lineage": "XBB.1", + "lineage_name": "XBB.1", + "representative_genome": "" + }, + "tags": [ + "XBB.1" + ], + "note": "Unique mutations for XBB.1 sublineage", + "sites": [ + "spike:R408S", + "spike:K417N", + "orf8:G8*" + ], + "rules": { + "min_alt": 1, + "max_ref": 1 + } +} diff --git a/constellations/definitions/cXBB.json b/constellations/definitions/cXBB.json new file mode 100644 index 0000000..6395fe7 --- /dev/null +++ b/constellations/definitions/cXBB.json @@ -0,0 +1,41 @@ +{ + "label": "Omicron (XBB-like)", + "description": "XBB recombinant lineage defining mutations", + "sources": [ + ], + "type": "variant", + "variant": { + "Pango_lineages": [ + "XBB" + ], + "WHO_label": "Omicron", + "parent_lineage": "XBB-parent2", + "mrca_lineage": "XBB", + "lineage_name": "XBB", + "representative_genome": "" + }, + "tags": [ + "XBB" + ], + "note": "Unique mutations for XBB sublineage", + "sites": [ + "spike:V83A", + "spike:Y144-", + "spike:H146Q", + "spike:Q183E", + "spike:V213E", + "spike:R346T", + "spike:L368I", + "spike:V445P", + "spike:F486S", + "spike:F490S", + + "nuc:C15738T", + "nuc:T15939C", + "nuc:T17859C" + ], + "rules": { + "min_alt": 5, + "max_ref": 3 + } +}