Elevation criteria

In India, XBB.1.16 has reached a share of around 75% in samples collected mid March.

In all Asian sequences in GISAID at time of writing, XBB.1.16 represents around 10% of all sequences collected mid March.

A simple logistical growth model shows an absolute daily growth advantage of around 9% in all of Asia.

The relative growth against all of XBB* is around 5% in India.

Similar advantages are also apparent in the US.

XBB.1.16 hence clearly satisfies criterion 4 of the most recent Nextstrain clade naming criteria ("A clade shows consistent >0.05 per day growth in frequency where it’s circulating and has reached >5% regional frequency", see https://next.nextstrain.org/blog/2022-04-29-SARS-CoV-2-clade-naming-2022).

Also the additional requirement of "multiple mutations in S1 or particular mutations of known biological relevance." are satisfied, as compared to parental 22F (XBB), XBB.1.16 has 3 S1 mutations (180V, 478R, 486P) of which 2 are in the receptor binding domain and of known biological relevance (478R, 486P). While is already present in clade 23A (XBB.1.5), XBB.1.16 has evolved this substitution independently. What makes XBB.1.16 distinct is the additional substitution 478R.

Share of XBB.1.16 vs other clades over time in select countries (logit scale):

Absolute numbers of cases (to be taken with grain of salt due to changing testing) in select countries showing XBB.1.16 driving a wave in India (linear scale):

Log plot of absolute number of cases in select countries:

These were all created by @trvrb using https://github.com/blab/rt-from-frequency-dynamics/tree/master/results/omicron-xbb116

Here are some further plots of relative growth advantages of XBB.1.16 vs XBB*+486P (comprising all XBB.1.5-like lineages) via covSpectrum, showing that XBB.1.16 is not just another XBB.1.5 but appears to outcompete it, at least in those countries: (take exact numbers with big grain of salt, but trends and significance is clear)

from: https://cov-spectrum.org/explore/World/AllSamples/Past6M/variants?aaMutations=S%3A486P&nextcladePangoLineage=XBB*&variantQuery1=nextcladePangoLineage%3AXBB.1.16*&analysisMode=CompareToBaseline&

Checklist, from Slack:

• NCoV file updates
  • defaults/clade_emergence_dates.tsv
  • defaults/clade_hierarchy.tsv
  • defaults/clades.tsv
  • defaults/clades_nextstrain.tsv
  • defaults/color_ordering.tsv
  • defaults/emerging_lineages.tsv
  • changelog
• Explain in PR why we are elevating
• Start test build: will be at ".../open/23B/global/6m" etc, first builds should be there by 11am UTC
• Check test build
• Pass PR review
• Merge PR
• Update clade diagram figure
• Add new variant (with new name) to Nextclade dataset
• Trigger full runs on GISAID & Genbank once Nextclade updated
  • Add touch files
  • Ingest
  • Deactivate auto-triggered runs
  • Reactivate auto-triggered runs once ingest complete
• Update covariants
• Draft tweet
• Send tweet