Elevate XBB as 22F

[corneliusroemer]

Description of proposed changes

(Code changes @corneliusroemer, elevation reasons contributed by @trvrb)

This PR elevates Pango lineage XBB to Nextstrain clade 22F. Per cov-lineages.org, XBB is a "recombinant lineage of BJ.1 and BA.2.75 with breakpoint in S1". It possesses spike mutations:

V83A, H146Q, Q183E, V210I, G213E, R346T, L368I, V445P, F486S, F490S

XBB is now at 19% frequency in Asia in the standard 2m Asia-focused ncov build:

Applying the method from Figgins and Bedford, we estimate frequencies in Bangladesh, India and Singapore are now at 98%, 49% and 93% respectively:

And simple logistic growth rates have followed 0.21, 0.05 and 0.17 per day respectively.

If we look more broadly, we observe equivalent growth rates between BQ.1 and XBB in regions where they are co-circulating, this being Australia and the US.

It's too early to say whether BQ.1 or XBB will have a larger global impact, however, it's now clear that XBB meets our criteria 4 for designating a Nextstrain clade, namely:

A clade shows consistent >0.05 per day growth in frequency where it’s circulating and has reached >5% regional frequency

Edited by @trvrb Oct 23, 2022

Testing

Trial build results are available at https://nextstrain.org/staging/ncov/gisaid/trial/xbb-is-22F/asia/2m, etc...