Merge pull request #89 from nextstrain/update-pivot

Update Pango lineage pivots to JN.1
nextstrain · Feb 27, 2024 · 39a3f83 · 39a3f83
2 parents c96088f + 1f1d679
commit 39a3f83
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Showing 3 changed files with 9 additions and 9 deletions.
diff --git a/config/config.yaml b/config/config.yaml
@@ -58,17 +58,17 @@ models:
   gisaid:
     nextstrain_clades:
       global:
-        pivot: "23A"
+        pivot: "23I"
     pango_lineages:
       global:
-        pivot: "XBB.1.5"
+        pivot: "JN.1"
   open:
     nextstrain_clades:
       global:
-        pivot: "23A"
+        pivot: "23I"
     pango_lineages:
       global:
-        pivot: "XBB.1.5"
+        pivot: "JN.1"
 
 # Model configs
 mlr_config: "config/mlr-config.yaml"

diff --git a/config/mlr-config.yaml b/config/mlr-config.yaml
@@ -13,7 +13,7 @@ settings:
 
 model:
   generation_time: 4.8
-  pivot: "23A"
+  pivot: "23I"
   hierarchical: true
 
 inference:

diff --git a/viz/src/App.jsx b/viz/src/App.jsx
@@ -41,8 +41,8 @@ function App() {
         <h2>Clade growth advantage</h2>
         <p>
           These plots show the estimated growth advantage for given clades relative to clade
-          23A (lineage XBB.1.5). This describes how many more secondary infections a variant causes
-          on average relative to clade 23A. Vertical bars show the 95% HPD. The "hierarchical" panel
+          23I (lineage BA.2.86). This describes how many more secondary infections a variant causes
+          on average relative to clade 23I. Vertical bars show the 95% HPD. The "hierarchical" panel
           shows pooled estimate of growth rates across different locations.
           Results last updated {mlrCladesData?.modelData?.get('updated') || 'loading'}.
         </p>
@@ -64,8 +64,8 @@ function App() {
         <h2>Lineage growth advantage</h2>
         <p>
           These plots show the estimated growth advantage for given Pango lineages relative to
-          lineage XBB.1.5. This describes how many more secondary infections a variant causes
-          on average relative to lineage XBB.1.5. Vertical bars show the 95% HPD.
+          lineage JN.1. This describes how many more secondary infections a variant causes
+          on average relative to lineage JN.1. Vertical bars show the 95% HPD.
           The "hierarchical" panel shows pooled estimate of growth rates across different locations.
           Results last updated {mlrLineagesData?.modelData?.get('updated') || 'loading'}.
         </p>