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Update Pango lineage pivots to JN.1
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Based on @trvrb's notes¹ in today's forecasting meeting:

> Separately, we need to still update the pivot soon as XBB.1.5
> frequencies are becoming quite low in early timesteps. Based on
> previous input, we should just plan to jump directly to JN.1 as baseline.

We don't have an exact matching Nextstrain clade for JN.1 so not
updating the pivot for Nextstrain clades in this commit.

¹ https://docs.google.com/document/d/1XFEsF170v-Vof72qZDdjFD3yfT57VbiJBX83h6-becg
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joverlee521 committed Feb 26, 2024
1 parent c96088f commit 033fd45
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Showing 2 changed files with 4 additions and 4 deletions.
4 changes: 2 additions & 2 deletions config/config.yaml
Original file line number Diff line number Diff line change
Expand Up @@ -61,14 +61,14 @@ models:
pivot: "23A"
pango_lineages:
global:
pivot: "XBB.1.5"
pivot: "JN.1"
open:
nextstrain_clades:
global:
pivot: "23A"
pango_lineages:
global:
pivot: "XBB.1.5"
pivot: "JN.1"

# Model configs
mlr_config: "config/mlr-config.yaml"
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4 changes: 2 additions & 2 deletions viz/src/App.jsx
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Expand Up @@ -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>
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