diff --git a/config/config.yaml b/config/config.yaml index d109d56..be836b4 100644 --- a/config/config.yaml +++ b/config/config.yaml @@ -58,14 +58,14 @@ models: gisaid: nextstrain_clades: global: - pivot: "23I" + pivot: "24A" pango_lineages: global: pivot: "JN.1" open: nextstrain_clades: global: - pivot: "23I" + pivot: "24A" pango_lineages: global: pivot: "JN.1" @@ -93,46 +93,54 @@ mlr_config: "config/mlr-config.yaml" # * Lineages which are not a descendant of a clade-defining lineage will be # grouped as 'other' clade_definitions: + - clade: "24B" + display_name: "24B (JN.1.11.1)" + defining_lineage: "JN.1.11.1" + color: '#DC2F24' + - clade: "24A" + display_name: "24A (JN.1)" + defining_lineage: "JN.1" + color: '#E4632E' - clade: "23I" display_name: "23I (BA.2.86)" defining_lineage: "BA.2.86" - color: '#DC2F24' + color: '#E69136' - clade: "23H" display_name: "23H (HK.3)" defining_lineage: "HK.3" - color: '#E56C2F' + color: '#D9AD3D' - clade: "23G" display_name: "23G (XBB.1.5.70)" defining_lineage: "XBB.1.5.70" - color: '#E39B39' + color: '#C1BA47' - clade: "23F" display_name: "23F (EG.5.1)" defining_lineage: "EG.5.1" - color: '#CEB541' + color: '#A2BE57' - clade: "23E" display_name: "23E (XBB.2.3)" defining_lineage: "XBB.2.3" - color: '#ADBD51' + color: '#83BA70' - clade: "23D" display_name: "23D (XBB.1.9)" defining_lineage: "XBB.1.9" - color: '#88BB6C' + color: '#69B091' - clade: "23C" display_name: "23C (CH.1.1)" defining_lineage: "CH.1.1" - color: '#69B091' + color: '#549DB2' - clade: "23B" display_name: "23B (XBB.1.16)" defining_lineage: "XBB.1.16" - color: '#5199B7' + color: '#4580CA' - clade: "22F" display_name: "22F (XBB)" defining_lineage: "XBB" - color: '#4042C7' + color: '#3E58CF' - clade: "23A" display_name: "23A (XBB.1.5)" defining_lineage: "XBB.1.5" - color: '#4274CE' + color: '#462EB9' - clade: "other" display_name: "other" defining_lineage: False diff --git a/config/mlr-config.yaml b/config/mlr-config.yaml index 3ebdf34..3ded58b 100644 --- a/config/mlr-config.yaml +++ b/config/mlr-config.yaml @@ -13,7 +13,7 @@ settings: model: generation_time: 4.8 - pivot: "23I" + pivot: "24A" hierarchical: true inference: diff --git a/viz/src/App.jsx b/viz/src/App.jsx index cdb9065..c05843f 100644 --- a/viz/src/App.jsx +++ b/viz/src/App.jsx @@ -41,8 +41,8 @@ function App() {

Clade growth advantage

These plots show the estimated growth advantage for given clades relative to clade - 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 + 24A (lineage JN.1). This describes how many more secondary infections a variant causes + on average relative to clade 24A. 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'}.