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nextstrain / forecasts-ncov

SARS-CoV-2 variant growth rates and frequency forecasts
https://nextstrain.org/sars-cov-2/forecasts/
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Update clade definitions #108

Closed trvrb closed 2 months ago

trvrb commented 2 months ago

Previous clades including 23B, 23C, ..., 23I are all now extinct or rare enough that extant examples are getting lumped into the "other" bin. With the current clade definitions these extinct clades are taking up all the color bandwidth and the three relevant clades of 24A, 24B and 24C are all similar shades of red.

This commit removes extinct clades and updates colors for surviving clades.

Clade frequencies on main

Screenshot 2024-09-11 at 12 59 33 PM

Clade frequencies with PR

ncov_forecasts_clades_2024_09_09

Lineage growth advantages on main

Screenshot 2024-09-11 at 1 01 01 PM

Lineage growth advantages with PR

Screenshot 2024-09-11 at 1 01 55 PM

@joverlee521 or @jameshadfield, could you take a quick look at this?

trvrb commented 2 months ago

Thanks!

I assume the upcoming https://github.com/nextstrain/ncov/pull/1149 will be added later as red?

Yeah. As new clades get added (and old clades die out), we're going to need to keep manually updating clade_definitions in the config.