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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 Pango lineage pivots to JN.1 #89

Closed joverlee521 closed 6 months ago

joverlee521 commented 6 months ago

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

Checklist

joverlee521 commented 6 months ago

Making this a draft PR in case we want to wait on making JN.1 it's own Nextstrain clade before changing the pivots.

joverlee521 commented 6 months ago

Test model run with new pivots

joverlee521 commented 6 months ago

Test run completed successfully. See results in test app:

trvrb commented 6 months ago

Brilliant! Thank you Jover for pulling this together.

joverlee521 commented 6 months ago

Running the model on this branch to be deployed to production. Once the run is complete, I will merge this PR to update the front-end viz.