add some xbb

cov-lineages · May 23, 2023 · a804602 · a804602
1 parent 61e2a6b
commit a804602
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Showing 8 changed files with 195 additions and 5 deletions.
diff --git 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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
+    }
+}