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Update Nextstrain clade pivots to 23I (BA.2.86)
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Based on @trvrb's feedback on Slack¹

> I think the thing to do here is to update clade pivot to 23I and
> update the lineage pivot to JN.1. It's not at all essential that
> they're completely synonymous.

The previous commit already updated the Pango lineage pivot to JN.1,
so this commit updates the Nextstrain clade pivot to 23I (BA.2.86).

¹ https://bedfordlab.slack.com/archives/C036L7V615F/p1708992783913369?thread_ts=1708990294.255439&cid=C036L7V615F
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joverlee521 committed Feb 27, 2024
1 parent 033fd45 commit 1f1d679
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Showing 3 changed files with 5 additions and 5 deletions.
4 changes: 2 additions & 2 deletions config/config.yaml
Original file line number Diff line number Diff line change
Expand Up @@ -58,14 +58,14 @@ models:
gisaid:
nextstrain_clades:
global:
pivot: "23A"
pivot: "23I"
pango_lineages:
global:
pivot: "JN.1"
open:
nextstrain_clades:
global:
pivot: "23A"
pivot: "23I"
pango_lineages:
global:
pivot: "JN.1"
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2 changes: 1 addition & 1 deletion config/mlr-config.yaml
Original file line number Diff line number Diff line change
Expand Up @@ -13,7 +13,7 @@ settings:

model:
generation_time: 4.8
pivot: "23A"
pivot: "23I"
hierarchical: true

inference:
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4 changes: 2 additions & 2 deletions viz/src/App.jsx
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Expand Up @@ -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>
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