Elevate lineage BQ.1 to clade 22E

[trvrb]

Description of proposed changes

This commit elevates lineage BQ.1 as clade 22E. BQ.1 is Pango lineage BA.5.3.1.1.1.1.1 that bears mutations at ORF1a: Q556K, L3829F, ORF1b: Y264H, M1156I, ORF9b: S10F, N: E136D, and spike K444T and N460K.

Mutational path leading to BQ.1 can be seen at nextstrain.org/nextclade/sars-cov-2 and is copied below:

BQ.1 has been rapidly going in frequency across multiple geographies. If we apply method from Figgins and Bedford, 2022, medRxiv we can estimate growth rates across lineages. Currently the US has the most recent sequencing data (31k sequences from the previous 30 days) which allows estimates of lineage-level Rt. Figures below are borrowed from github.com/blab/rt-from-frequency-dynamics/tree/master/results/pango-countries:

BQ.1 here combines both BQ.1 and BQ.1.1 for more power in analysis and shows that they are currently handily above other lineages in the US. We estimate current BQ.1 frequency in the US to be about 6.5% with a lineage-specific Rt of 1.35 and logit frequency growth of 0.11 per day.

Furthermore, we see this pattern of rapid growth of BQ.1 repeated in other geographies. The following uses geographies that have sufficient sequencing data and specifically breaks out BA.2.75.2, BQ.1, BQ.1.1 and XBB. Figures below are borrowed here github.com/blab/rt-from-frequency-dynamics/tree/master/results/omicron-ba275:

BQ.1 hits our clade designation criteria 4:

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

Testing

This PR is running now and output will be available at nextstrain.org/staging/ncov/gisaid/trial/clade-22E/global/2m, etc... shortly.

Release checklist

• Update docs/src/reference/change_log.md in this pull request to document these changes by the date they were added.

[corneliusroemer]

The first BQ.1 could potentially have already appeared quite some time before July, first samples from Nigeria are early July, but given low sampling there it must have been around for a few months already.

Depends how tight we want to be. Global circulation started to become apparent early August.

https://cov-spectrum.org/explore/World/AllSamples/Past6M/variants/international-comparison?nextcladePangoLineage=BQ.1*&

[corneliusroemer]

Convincing case for elevating BQ.1*, which has a very significant growth advantage as shown in various other analyses (e.g. also Tom Wenseleers and Moritz Gerstung, using UK data, German data and global data),
https://twitter.com/MoritzGerstung/status/1580222575866564608?s=20&t=9GbdKDdIKv_sT8mNr2ZBog

[trvrb]

The trial builds worked well. Additionally, latest Pango designations show a diversity of BQ.1* viruses (up to BQ.1.17). Even if BQ.1.1 is currently slowly overtaking BQ.1, it's not clear that another BQ.1 sub-lineage won't emerge that's more competitive.

BQ.1 has clade 22E should be the safer bet. I'm going to merge this now. It should get deployed tomorrow by automated rebuilds.