From 033fd456c258207eefc7a39319e131a4408be714 Mon Sep 17 00:00:00 2001 From: Jover Lee Date: Mon, 26 Feb 2024 15:06:51 -0800 Subject: [PATCH] Update Pango lineage pivots to JN.1 MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit 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 --- config/config.yaml | 4 ++-- viz/src/App.jsx | 4 ++-- 2 files changed, 4 insertions(+), 4 deletions(-) diff --git a/config/config.yaml b/config/config.yaml index 7f52f13..0d6f3e6 100644 --- a/config/config.yaml +++ b/config/config.yaml @@ -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" diff --git a/viz/src/App.jsx b/viz/src/App.jsx index 33045f8..512d81c 100644 --- a/viz/src/App.jsx +++ b/viz/src/App.jsx @@ -64,8 +64,8 @@ function App() {

Lineage growth advantage

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'}.