flu: update subclade of H3N2/HA

nextstrain · Dec 20, 2023 · 3660c69 · 3660c69
1 parent f60dac9
commit 3660c69
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Showing 12 changed files with 53 additions and 34 deletions.
diff --git a/data/nextstrain/flu/h1n1pdm/ha/CY121680/pathogen.json b/data/nextstrain/flu/h1n1pdm/ha/CY121680/pathogen.json
@@ -80,6 +80,10 @@
   },
   "nucMutLabelMap": {},
   "nucMutLabelMapReverse": {},
+  "shortcuts": [
+    "flu-h1n1pdm-ha-broad",
+    "nextstrain/flu/h1n1pdm/ha/california-7-2009"
+  ],
   "aaMotifs": [
     {
       "name": "glycosylation",
@@ -111,8 +115,5 @@
     "segment": "ha",
     "reference accession": "CY121680",
     "reference name": "A/California/7/2009-egg"
-  },
-  "version": {
-    "tag": "unreleased"
   }
-}
+}
diff --git a/data/nextstrain/flu/h1n1pdm/ha/MW626062/pathogen.json b/data/nextstrain/flu/h1n1pdm/ha/MW626062/pathogen.json
@@ -80,6 +80,12 @@
   },
   "nucMutLabelMap": {},
   "nucMutLabelMapReverse": {},
+  "shortcuts": [
+    "flu-h1n1pdm-ha",
+    "nextstrain/flu/h1n1pdm",
+    "nextstrain/flu/h1n1pdm/ha",
+    "nextstrain/flu/h1n1pdm/ha/wisconsin-588-2019"
+  ],
   "aaMotifs": [
     {
       "name": "glycosylation",
@@ -111,8 +117,5 @@
     "segment": "ha",
     "reference accession": "MW626062",
     "reference name": "A/Wisconsin/588/2019"
-  },
-  "version": {
-    "tag": "unreleased"
   }
-}
+}
diff --git a/data/nextstrain/flu/h1n1pdm/na/MW626056/pathogen.json b/data/nextstrain/flu/h1n1pdm/na/MW626056/pathogen.json
@@ -79,6 +79,11 @@
   },
   "nucMutLabelMap": {},
   "nucMutLabelMapReverse": {},
+  "shortcuts": [
+    "flu-h1n1pdm-na",
+    "nextstrain/flu/h1n1pdm/na",
+    "nextstrain/flu/h1n1pdm/na/wisconsin-588-2019"
+  ],
   "aaMotifs": [
     {
       "name": "glycosylation",
@@ -106,8 +111,5 @@
     "segment": "na",
     "reference accession": "MW626056",
     "reference name": "A/Wisconsin/588/2019"
-  },
-  "version": {
-    "tag": "unreleased"
   }
-}
+}
diff --git a/data/nextstrain/flu/h3n2/ha/CY163680/CHANGELOG.md b/data/nextstrain/flu/h3n2/ha/CY163680/CHANGELOG.md
@@ -2,6 +2,7 @@
 
 Initial release for Nextclade v3!
 
+ - Addition of subclade H.1, H.2, H.3, and H.4
  - Aliasing of G.1.3.1.1 as subclade H
 
 Read more about Nextclade datasets in the documentation: https://docs.nextstrain.org/projects/nextclade/en/stable/user/datasets.html
diff --git a/data/nextstrain/flu/h3n2/ha/CY163680/pathogen.json b/data/nextstrain/flu/h3n2/ha/CY163680/pathogen.json
@@ -80,6 +80,10 @@
   },
   "nucMutLabelMap": {},
   "nucMutLabelMapReverse": {},
+  "shortcuts": [
+    "flu-h3n2-ha-broad",
+    "nextstrain/flu/h3n2/ha/wisconsin-67-2005"
+  ],
   "aaMotifs": [
     {
       "name": "glycosylation",
@@ -111,8 +115,5 @@
     "segment": "ha",
     "reference accession": "CY163680",
     "reference name": "A/Wisconsin/67/2005-egg"
-  },
-  "version": {
-    "tag": "unreleased"
   }
-}
+}
diff --git a/data/nextstrain/flu/h3n2/ha/CY163680/tree.json b/data/nextstrain/flu/h3n2/ha/CY163680/tree.json
diff --git a/data/nextstrain/flu/h3n2/ha/EPI1857216/CHANGELOG.md b/data/nextstrain/flu/h3n2/ha/EPI1857216/CHANGELOG.md
@@ -2,6 +2,7 @@
 
 Initial release for Nextclade v3!
 
+ - Addition of subclade H.1, H.2, H.3, and H.4
  - Aliasing of G.1.3.1.1 as subclade H
 
 Read more about Nextclade datasets in the documentation: https://docs.nextstrain.org/projects/nextclade/en/stable/user/datasets.html
diff --git a/data/nextstrain/flu/h3n2/ha/EPI1857216/pathogen.json b/data/nextstrain/flu/h3n2/ha/EPI1857216/pathogen.json
@@ -80,6 +80,12 @@
   },
   "nucMutLabelMap": {},
   "nucMutLabelMapReverse": {},
+  "shortcuts": [
+    "flu-h3n2-ha",
+    "nextstrain/flu/h3n2",
+    "nextstrain/flu/h3n2/ha",
+    "nextstrain/flu/h3n2/ha/darwin-6-2021"
+  ],
   "phenotypeData": [
     {
       "name": "RBD",
@@ -157,8 +163,5 @@
     "segment": "ha",
     "reference accession": "EPI1857216",
     "reference name": "A/Darwin/6/2021"
-  },
-  "version": {
-    "tag": "unreleased"
   }
-}
+}
diff --git a/data/nextstrain/flu/h3n2/ha/EPI1857216/tree.json b/data/nextstrain/flu/h3n2/ha/EPI1857216/tree.json
diff --git a/data/nextstrain/flu/h3n2/na/EPI1857215/pathogen.json b/data/nextstrain/flu/h3n2/na/EPI1857215/pathogen.json
@@ -79,6 +79,11 @@
   },
   "nucMutLabelMap": {},
   "nucMutLabelMapReverse": {},
+  "shortcuts": [
+    "flu-h3n2-na",
+    "nextstrain/flu/h3n2/na",
+    "nextstrain/flu/h3n2/na/darwin-6-2021"
+  ],
   "aaMotifs": [
     {
       "name": "glycosylation",
@@ -106,8 +111,5 @@
     "segment": "na",
     "reference accession": "EPI1857215",
     "reference name": "A/Darwin/6/2021"
-  },
-  "version": {
-    "tag": "unreleased"
   }
-}
+}
diff --git a/data/nextstrain/flu/vic/ha/KX058884/pathogen.json b/data/nextstrain/flu/vic/ha/KX058884/pathogen.json
@@ -80,6 +80,12 @@
   },
   "nucMutLabelMap": {},
   "nucMutLabelMapReverse": {},
+  "shortcuts": [
+    "flu-vic-ha",
+    "nextstrain/flu/vic",
+    "nextstrain/flu/vic/ha",
+    "nextstrain/flu/vic/ha/brisbane-60-2008"
+  ],
   "aaMotifs": [
     {
       "name": "glycosylation",
@@ -111,8 +117,5 @@
     "segment": "ha",
     "reference accession": "KX058884",
     "reference name": "B/Brisbane/60/2008-egg"
-  },
-  "version": {
-    "tag": "unreleased"
   }
-}
+}
diff --git a/data/nextstrain/flu/vic/na/CY073894/pathogen.json b/data/nextstrain/flu/vic/na/CY073894/pathogen.json
@@ -79,6 +79,11 @@
   },
   "nucMutLabelMap": {},
   "nucMutLabelMapReverse": {},
+  "shortcuts": [
+    "flu-vic-na",
+    "nextstrain/flu/vic/na",
+    "nextstrain/flu/vic/na/brisbane-60-2008"
+  ],
   "aaMotifs": [
     {
       "name": "glycosylation",
@@ -106,8 +111,5 @@
     "segment": "na",
     "reference accession": "CY073894",
     "reference name": "B/Brisbane/60/2008"
-  },
-  "version": {
-    "tag": "unreleased"
   }
-}
+}