diff --git a/scripts/approx_first_dates.py b/scripts/approx_first_dates.py index 8d5692bc8..1b186fb78 100644 --- 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 index 98620d7c6..2aac7844c 100644 --- 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 index 9b199608b..bbfbe9758 100644 --- 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