From af8a84a8659d8b2ec8973f5baed8d3f3e4567919 Mon Sep 17 00:00:00 2001 From: AshleyShalloe <54893285+AshleyShalloe@users.noreply.github.com> Date: Wed, 8 Jun 2022 12:04:37 +0100 Subject: [PATCH] Updated PHE_label and tags with new nomenclature --- constellations/definitions/cA.23.1+E484K.json | 7 ++++--- constellations/definitions/cAV1.json | 5 +++-- constellations/definitions/cAY.4.2.json | 7 ++++--- constellations/definitions/cB.1.1.318.json | 7 ++++--- constellations/definitions/cB.1.525.json | 7 ++++--- constellations/definitions/cB.1.617.1.json | 7 ++++--- constellations/definitions/cB.1.617.3.json | 5 +++-- constellations/definitions/cBA.1.json | 6 ++++-- constellations/definitions/cBA.2.json | 6 ++++-- constellations/definitions/cBA.4.json | 4 +++- constellations/definitions/cBA.5.json | 6 ++++-- constellations/definitions/cC.37.json | 4 +++- constellations/definitions/cP.2.json | 5 +++-- constellations/definitions/cP.3.json | 7 ++++--- constellations/definitions/cXE.json | 8 +++++--- 15 files changed, 56 insertions(+), 35 deletions(-) diff --git a/constellations/definitions/cA.23.1+E484K.json b/constellations/definitions/cA.23.1+E484K.json index 0e4bea2..74f69ab 100644 --- a/constellations/definitions/cA.23.1+E484K.json +++ b/constellations/definitions/cA.23.1+E484K.json @@ -9,14 +9,15 @@ "Pango_lineages": [ "A.23.1" ], - "mrca_lineage": "A.23.1", - "PHE_label": "VUI-21FEB-01", + "mrca_lineage": "A.23.1", + "PHE_label": "V-21FEB-01", "representative_genome": "" }, "tags": [ "A.23.1", "VUI-21FEB-01", - "VUI202102/01" + "VUI202102/01", + "V-21FEB-01" ], "sites": [ "nsp3:L741F", diff --git a/constellations/definitions/cAV1.json b/constellations/definitions/cAV1.json index 4e37449..68562a8 100644 --- a/constellations/definitions/cAV1.json +++ b/constellations/definitions/cAV1.json @@ -9,11 +9,12 @@ "AV.1" ], "mrca_lineage": "AV.1", - "PHE_label": "VOC-20-DEC-01", + "PHE_label": "VOC-20DEC-01", "representative_genome": "" }, "tags": [ - "AV.1" + "AV.1", + "VOC-20DEC-01" ], "sites": [ "s:D80G", diff --git a/constellations/definitions/cAY.4.2.json b/constellations/definitions/cAY.4.2.json index 900788f..6d5a150 100644 --- a/constellations/definitions/cAY.4.2.json +++ b/constellations/definitions/cAY.4.2.json @@ -6,16 +6,17 @@ "type": "variant", "variant": { "Pango_lineages": [ - "AY.4.2" + "AY.4.2" ], "mrca_lineage": "AY.4.2", "lineage_name": "AY.4.2", "parent_lineage": "AY.4", - "PHE_label": "VUI-21OCT-01", + "PHE_label": "V-21OCT-01", "representative_genome": "" }, "tags": [ - "AY.4.2" + "AY.4.2", + "V-21OCT-01" ], "sites": [ "nuc:T17040C", diff --git a/constellations/definitions/cB.1.1.318.json b/constellations/definitions/cB.1.1.318.json index a93e4b5..b393f5c 100644 --- a/constellations/definitions/cB.1.1.318.json +++ b/constellations/definitions/cB.1.1.318.json @@ -9,14 +9,15 @@ "Pango_lineages": [ "B.1.1.318" ], - "mrca_lineage": "B.1.1.318", - "PHE_label": "VUI-21FEB-04", + "mrca_lineage": "B.1.1.318", + "PHE_label": "V-21FEB-04", "representative_genome": "" }, "tags": [ "B.1.1.318", "VUI-21FEB-04", - "VUI202102/04" + "VUI202102/04", + "V-21FEB-04" ], "sites": [ "nuc:C3961T", diff --git a/constellations/definitions/cB.1.525.json b/constellations/definitions/cB.1.525.json index b1e65ce..69daf3f 100644 --- a/constellations/definitions/cB.1.525.json +++ b/constellations/definitions/cB.1.525.json @@ -9,8 +9,8 @@ "Pango_lineages": [ "B.1.525" ], - "mrca_lineage": "B.1.525", - "PHE_label": "VUI-21FEB-03", + "mrca_lineage": "B.1.525", + "PHE_label": "V-21FEB-03", "WHO_label": "Eta", "representative_genome": "" }, @@ -20,7 +20,8 @@ "VUI202102/03", "Eta", "G/484K.V3", - "20A" + "20A", + "V-21FEB-03" ], "sites": [ "nuc:C1498T", diff --git a/constellations/definitions/cB.1.617.1.json b/constellations/definitions/cB.1.617.1.json index 18dfb33..e41f8ed 100644 --- a/constellations/definitions/cB.1.617.1.json +++ b/constellations/definitions/cB.1.617.1.json @@ -10,13 +10,14 @@ "Pango_lineages": [ "B.1.617.1" ], - "mrca_lineage": "B.1.617.1", - "PHE_label": "VUI-21APR-01", + "mrca_lineage": "B.1.617.1", + "PHE_label": "V-21APR-01", "representative_genome": "" }, "tags": [ "B.1.617.1", - "VUI-21APR-01" + "VUI-21APR-01", + "V-21APR-01" ], "sites": [ "nuc:C3457T", diff --git a/constellations/definitions/cB.1.617.3.json b/constellations/definitions/cB.1.617.3.json index c7564be..9cfdf0f 100644 --- a/constellations/definitions/cB.1.617.3.json +++ b/constellations/definitions/cB.1.617.3.json @@ -10,12 +10,13 @@ "B.1.617.3" ], "mrca_lineage": "B.1.617.3", - "PHE_label": "VUI-21APR-03", + "PHE_label": "V-21APR-03", "representative_genome": "" }, "tags": [ "B.1.617.3", - "VUI-21APR-03" + "VUI-21APR-03", + "V-21APR-03" ], "sites": [ "nuc:C835T", diff --git a/constellations/definitions/cBA.1.json b/constellations/definitions/cBA.1.json index 0ca3e5f..2b35463 100644 --- a/constellations/definitions/cBA.1.json +++ b/constellations/definitions/cBA.1.json @@ -9,13 +9,15 @@ "BA.1" ], "WHO_label": "Omicron", - "mrca_lineage": "BA.1", + "mrca_lineage": "BA.1", "lineage_name": "BA.1", "parent_lineage": "B.1.1.529", + "PHE_label": "VOC-21NOV-01", "representative_genome": "" }, "tags": [ - "BA.1" + "BA.1", + "VOC-21NOV-01" ], "sites": [ "orf1ab:K856R", diff --git a/constellations/definitions/cBA.2.json b/constellations/definitions/cBA.2.json index cb176b0..3d6c051 100644 --- a/constellations/definitions/cBA.2.json +++ b/constellations/definitions/cBA.2.json @@ -9,13 +9,15 @@ "BA.2" ], "WHO_label": "Omicron", - "mrca_lineage": "BA.2", + "mrca_lineage": "BA.2", "lineage_name": "BA.2", "parent_lineage": "B.1.1.529", + "PHE_label": "VOC-22JAN-01", "representative_genome": "" }, "tags": [ - "BA.2" + "BA.2", + "VOC-22JAN-01" ], "sites": [ "orf1ab:S135R", diff --git a/constellations/definitions/cBA.4.json b/constellations/definitions/cBA.4.json index 797f1f6..4370d5f 100644 --- a/constellations/definitions/cBA.4.json +++ b/constellations/definitions/cBA.4.json @@ -12,10 +12,12 @@ "mrca_lineage": "BA.4", "lineage_name": "BA.4", "parent_lineage": "B.1.1.529", + "PHE_label": "V-22APR-03", "representative_genome": "" }, "tags": [ - "BA.4" + "BA.4", + "V-22APR-03" ], "sites": [ "orf1ab:S135R", diff --git a/constellations/definitions/cBA.5.json b/constellations/definitions/cBA.5.json index d9665f7..3529ce2 100644 --- a/constellations/definitions/cBA.5.json +++ b/constellations/definitions/cBA.5.json @@ -9,13 +9,15 @@ "BA.5" ], "WHO_label": "Omicron", - "mrca_lineage": "BA.5", + "mrca_lineage": "BA.5", "lineage_name": "BA.5", "parent_lineage": "B.1.1.529", + "PHE_label": "V-22APR-04", "representative_genome": "" }, "tags": [ - "BA.5" + "BA.5", + "V-22APR-04" ], "sites": [ "orf1ab:S135R", diff --git a/constellations/definitions/cC.37.json b/constellations/definitions/cC.37.json index 5e7bca0..0711719 100644 --- a/constellations/definitions/cC.37.json +++ b/constellations/definitions/cC.37.json @@ -10,11 +10,13 @@ ], "mrca_lineage": "C.37", "WHO_label": "Lambda", + "PHE_label": "V-21JUN-01", "representative_genome": "" }, "tags": [ "Lambda", - "C.37" + "C.37", + "V-21JUN-01" ], "sites": [ "ORF1a:T1246I", diff --git a/constellations/definitions/cP.2.json b/constellations/definitions/cP.2.json index 28bab7b..031e398 100644 --- a/constellations/definitions/cP.2.json +++ b/constellations/definitions/cP.2.json @@ -10,14 +10,15 @@ "P.2" ], "mrca_lineage": "P.2", - "PHE_label": "VUI-21JAN-01", + "PHE_label": "V-21JAN-01", "WHO_label": "Zeta", "representative_genome": "" }, "tags": [ "P.2", "VUI-21JAN-01", - "VUI202101/01" + "VUI202101/01", + "V-21JAN-01" ], "sites": [ "ORF1ab:L205V", diff --git a/constellations/definitions/cP.3.json b/constellations/definitions/cP.3.json index 07dfe80..275326c 100644 --- a/constellations/definitions/cP.3.json +++ b/constellations/definitions/cP.3.json @@ -10,15 +10,16 @@ "Pango_lineages": [ "P.3" ], - "mrca_lineage": "P.3", - "PHE_label": "VUI-21MAR-02", + "mrca_lineage": "P.3", + "PHE_label": "V-21MAR-02", "WHO_label": "Theta", "representative_genome": "" }, "tags": [ "P.3", "VUI-21MAR-02", - "VUI202103/02" + "VUI202103/02", + "V-21MAR-02" ], "sites": [ "nsp3:D736G", diff --git a/constellations/definitions/cXE.json b/constellations/definitions/cXE.json index 9896cd5..e2e3469 100644 --- a/constellations/definitions/cXE.json +++ b/constellations/definitions/cXE.json @@ -9,14 +9,16 @@ "XE" ], "WHO_label": "Omicron", - "parent_lineage": "XE-parent2", - "mrca_lineage": "XE", + "parent_lineage": "XE-parent2", + "mrca_lineage": "XE", + "PHE_label": "V-22APR-02", "lineage_name": "XE", "representative_genome": "" }, "tags": [ "XE", - "GL2" + "GL2", + "V-22APR-02" ], "note": "Unique mutations for XE sublineage", "sites": [