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" 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 f627fa8..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", @@ -34,26 +35,26 @@ "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", "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..41d4ef2 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", @@ -41,24 +42,27 @@ "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": { "default": { - "min_alt": 18, + "min_alt": 28, "max_ref": 3, - "orf1ab:R5716C": "not ref" + "spike:Q493":"alt", + "n:P151":"ref", + "nuc:G27788":"ref" }, "Probable": { - "min_alt": 12, - "max_ref": 8, - "orf1ab:R5716C": "not ref" + "min_alt": 20, + "max_ref": 8 } } } diff --git a/constellations/definitions/cBA.3.json b/constellations/definitions/cBA.3.json index fd72dd6..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", @@ -36,21 +38,18 @@ "spike:G446S", "orf3a:T223V", "nuc:C26858T", + "n:RG203KR", "n:S413R" ], "note": "Unique mutations for sublineage", "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/cBA.4.json b/constellations/definitions/cBA.4.json new file mode 100644 index 0000000..25effd2 --- /dev/null +++ b/constellations/definitions/cBA.4.json @@ -0,0 +1,69 @@ +{ + "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:T3090I", + "nuc:C10198T", + "nuc:G10447A", + "del:11288:9", + "nuc:G12160A", + "nuc:C12880T", + "nuc:C15714T", + "orf1ab:R5716C", + "orf1ab:T6564I", + "nuc:A20055G", + "spike:T19I", + "s:HV69-", + "nuc:T22200G", + "spike:V213G", + "spike:S371F", + "spike:T376A", + "spike:D405N", + "spike:L452R", + "spike:F486V", + "nuc:C25000T", + "nuc:C25584T", + "nuc:C26060T", + "nuc:C26858T", + "orf6:D61L", + "nuc:G27788T", + "n:P151S", + "n:RG203KR", + "n:S413R" + ], + "note": "Unique mutations for sublineage", + "rules": { + "default": { + "min_alt": 30, + "max_ref": 5, + "m:D3N":"ref", + "s:Q493":"ref", + "orf6:D61":"not ref", + "n:P151S":"alt" + }, + "Probable": { + "min_alt": 20, + "max_ref": 8 + } + } +} diff --git a/constellations/definitions/cBA.5.json b/constellations/definitions/cBA.5.json new file mode 100644 index 0000000..d68f452 --- /dev/null +++ b/constellations/definitions/cBA.5.json @@ -0,0 +1,67 @@ +{ + "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:T3090I", + "nuc:C10198T", + "nuc:G10447A", + "del:11288:9", + "nuc:G12160A", + "nuc:C12880T", + "nuc:C15714T", + "orf1ab:R5716C", + "orf1ab:T6564I", + "nuc:A20055G", + "spike:T19I", + "s:HV69-", + "nuc:T22200G", + "spike:V213G", + "spike:S371F", + "spike:T376A", + "spike:D405N", + "spike:L452R", + "spike:F486V", + "nuc:C25000T", + "nuc:C25584T", + "nuc:C26060T", + "m:D3N", + "n:RG203KR", + "n:S413R" + ], + "note": "Unique mutations for sublineage", + "rules": { + "default": { + "min_alt": 28, + "max_ref": 5, + "s:Q493":"ref", + "nuc:C26858":"ref", + "nuc:G27788":"ref", + "n:P151":"ref", + "m:D3":"alt" + }, + "Probable": { + "min_alt": 20, + "max_ref": 8 + } + } +}