start to add 24A-C

hodcroftlab · Jul 19, 2024 · 0b11eba · 0b11eba
1 parent 399e10b
commit 0b11eba
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diff --git a/scripts/approx_first_dates.py b/scripts/approx_first_dates.py
@@ -32,6 +32,9 @@
     "23G": {"first_date": "2023-03-20"}, #omicron XBB.1.5.70
     "23H": {"first_date": "2023-06-15"}, #omicron HK.3
     "23I": {"first_date": "2023-08-01"}, #omicron BA.2.86
+    "24A": {"first_date": "2023-09-15"}, #omicron JN.1
+    "24B": {"first_date": "2024-02-01"}, #omicron JN.1.11.1
+    "24C": {"first_date": "2024-02-15"}, #omicron KP.3
     "Kappa": {"first_date": "2020-10-30"}, #Kappa
     "Delta417": {"first_date": "2020-10-30"}, #Delta plus (same as delta)
     "Eta": {"first_date": "2020-11-21"}, #Eta

diff --git a/scripts/cluster_analysis.py b/scripts/cluster_analysis.py
@@ -243,7 +243,7 @@ def print_all_clus_alerts(key):
 
 # Set a list of clades that are not yet in CoV, but are in Nextstrain - these need renaming to be part of their 'old' parent
 # until the clades can be added
-new_clades_to_rename = {"24A (Omicron)": "23I (Omicron)", "24B (Omicron)": "23I (Omicron)", "24C (Omicron":"23I (Omicron)"} #should be in format of Nexttrain_clade or column used to decide clade (Currently "23A (Omicron)")
+new_clades_to_rename = {} #should be in format of Nexttrain_clade or column used to decide clade (Currently "23A (Omicron)", example entry: "24A (Omicron)": "23I (Omicron)")
 if new_clades_to_rename:
     print("\n!!!!!!!!!!!!!!!!!!")
     print("There are currently clades that will be renamed!!:")

diff --git a/scripts/clusters.py b/scripts/clusters.py
@@ -3064,6 +3064,99 @@
         },
     },
 
+    "24A": {  #JN.1
+       "snps": [3565,18894,22926,27810],  # CTCC
+       "snps_with_base": ["T3565C","C18894T","T22926C","T27810C"], #MUST ADD VALUE WHEN TURN INTO PAGE!  
+       "cluster_data": [],
+       "nextstrain_build": True,
+       "parent": "23I.Omicron", 
+       "use_pango": True,
+       "has_no_page": True,
+       "type": "variant",
+       "graphing": True,
+       "important": True,
+       "country_info": [],
+       "col": "#29a4ef", 
+       "display_name": "24A (Omicron)",
+       "alt_display_name": ["JN.1"],
+       "build_name": "24A.Omicron",
+       "who_name": ["Omicron"],
+       "old_build_names": [],
+       "nextstrain_name": "24A",
+       "pango_lineages": [
+           {"name": "JN.1", "url": "https://cov-lineages.org/lineage.html?lineage=JN.1"},
+       ],
+       "nextstrain_url": "https://nextstrain.org/groups/neherlab/ncov/24A.Omicron",
+        "mutations": {
+            "nonsynonymous": [
+            ],
+            "synonymous": [
+            ],
+        },
+    },
+
+    "24B": {  #JN.1.11.1
+       "snps": [7113,17334,22928,24872,27810],  # TTCTC
+       "snps_with_base": ["7113T","17334T","22928C","24872T","27810C"], #MUST ADD VALUE WHEN TURN INTO PAGE!  
+       "cluster_data": [],
+       "nextstrain_build": True,
+       "parent": "24A.Omicron", 
+       "use_pango": True,
+       "has_no_page": True,
+       "type": "variant",
+       "graphing": True,
+       "important": True,
+       "country_info": [],
+       "col": "#6829ef", 
+       "display_name": "24B (Omicron)",
+       "alt_display_name": ["JN.1.11.1"],
+       "build_name": "24B.Omicron",
+       "who_name": ["Omicron"],
+       "old_build_names": [],
+       "nextstrain_name": "24B",
+       "pango_lineages": [
+           {"name": "JN.1.11.1", "url": "https://cov-lineages.org/lineage.html?lineage=JN.1.11.1"},
+       ],
+       "nextstrain_url": "https://nextstrain.org/groups/neherlab/ncov/24B.Omicron",
+        "mutations": {
+            "nonsynonymous": [
+            ],
+            "synonymous": [
+            ],
+        },
+    },
+
+    "24C": {  #KP.3
+       "snps": [7113,17334,22928,24872,27810],  # TTCTC
+       "snps_with_base": ["7113T","17334T","22928C","24872T","27810C"], #MUST ADD VALUE WHEN TURN INTO PAGE!  
+       "cluster_data": [],
+       "nextstrain_build": True,
+       "parent": "24B.Omicron", 
+       "use_pango": True,
+       "has_no_page": True,
+       "type": "variant",
+       "graphing": True,
+       "important": True,
+       "country_info": [],
+       "col": "#331eee", 
+       "display_name": "24C (Omicron)",
+       "alt_display_name": ["KP.3"],
+       "build_name": "24C.Omicron",
+       "who_name": ["Omicron"],
+       "old_build_names": [],
+       "nextstrain_name": "24C",
+       "pango_lineages": [
+           {"name": "KP.3", "url": "https://cov-lineages.org/lineage.html?lineage=KP.3"},
+       ],
+       "nextstrain_url": "https://nextstrain.org/groups/neherlab/ncov/24C.Omicron",
+        "mutations": {
+            "nonsynonymous": [
+            ],
+            "synonymous": [
+            ],
+        },
+    },
+
     # variant  -- part of 'Indian' in media - B.1.617.1
     "Kappa": {
         "snps": [17523, 23604, 22917],  # ORF1b:1352, S:681, 452