Merge pull request #60 from cov-lineages/dev

Adding in XE parent cascade lineage definitions and removing the probably BA.4 and BA.5 definition.

constellations/definitions/cXE-parent1.json

@@ -0,0 +1,31 @@
+{
+    "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": 3,
+        "max_ref": 0
+      }
+    }
+}

constellations/definitions/cXE-parent2.json

@@ -0,0 +1,46 @@
+{
+    "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": 9,
+        "max_ref": 3
+      }
+    }
+}

constellations/definitions/cXE.json

@@ -0,0 +1,33 @@
+{
+    "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:C3241T",
+    "nuc:T5386G",
+	"nuc:C14599T",
+    "nuc:C12880T",
+    "nuc:A29510C"
+    ],
+    "rules": {
+        "min_alt": 2,
+        "max_ref": 0
+    }
+}