Based on their frequencies and rate of growth, we've designated 4 new Nextstrain clades from @PangoNetwork lineages:
23C (CH.1.1)
23D (XBB.1.9)
23E (XBB.2.3)
23F (EG.5.1)
1/9
23C (CH.1.1) is a sublineage of 22D (BA.2.75) with additional spike RBD mutations at 346T, 444T, 452R & 486S. This non-XBB lineage has persisted despite the dominance of XBB descendants.
Currently most prevalent in Australia & New Zealand, it is also growing in Europe.
2/9
23D (XBB.1.9) is primarily characterized by mutations in ORF1a and ORF9b.
While it does not have S:486P, its 2 main sublineages (XBB.1.9.1 & XBB.1.9.2) do & are most common. Since the sublineages differ only by synonymous mutations, we decided to designate the parent.
Based on its rapid growth, particularly in Asia, we've designated the recombinant @PangoNetwork lineage XBB.1.16 & its descendants as clade 23B, labeled "23B (Omicron)" on Nextstrain trees.
Like 23A, 23B is a descendant of the recombinant 22F (XBB).
1/9
23B (XBB.1.16) is different from 22F (XBB) primarily through 3 new Spike mutations - S:E180V; S:K478R; & S:486P (acquired independently from other XBB sublineages).
In addition, S:G252V is inherited from ancestral XBB.1
S:486P is already known to confer an advantage as in 23A / XBB.1.5.
What sets 23B apart is the additional receptor binding domain mutation S:478R. Any potential impact of S:180V is less clear.
3/9
Based on its rapid growth in multiple geographies, we've designated the recombinant @PangoNetwork lineage XBB.1.5 & its descendants as clade 23A, labelled "23A (Omicron)" on Nextstrain trees.
23A (XBB.1.5) is a descendant of the recombinant 22F (XBB).
1/7
23A (XBB.1.5) is different from 22F (XBB) primarily through 2 new Spike muts - 1 in ancestor XBB.1 (S:G252V), & 1 in 23A itself S:486S -> S:486P. This 'P' change is associated with an increased ACE2 binding, which is likely why 23A is spreading.
Based on its rapid growth in multiple geographies, we've designed the recombinant @PangoNetwork lineage XBB & its descendants as clade 22F, labelled "22F (Omicron)" on Nextstrain trees.
Because 22F is a recombinant, its phylogenetic placement doesn't reflect its history.
1/5
22F/XBB is the result of a recombination between BJ.1 (BA.2.10.1.1) & BM.1.1.1 (BA.2.75.3.1.1.1) with breakpoint in S1 (first part of spike).
Recombination occurs during co-infection with 2 different variants, when parts of two different genomes end up together.
2/5
We can see the two 'parents' of 22F/XBB on the Nextclade phylogeny - parts of each of these genomes have combined to create a variant that has unique mutations from each parent lineage.
Based on its rapid growth in multiple geographies, we've designed @PangoNetwork lineage BQ.1 and descendants (most notably BQ.1.1) as clade 22E, labelled as "22E (Omicron)" on Nextstrain trees.
1/4
Clade 22E (lineage BQ.1) has been growing in frequency at a rate of 0.11 per day in USA, which is equivalent to the initial growth of 22B (BA.5) in the US & UK.
5-15% of recent samples in the USA & many countries in Europe are 22E & it might soon dominate in some places.
2/4
These growth dynamics, along with mutational profile, strongly suggest this clade will continue to spread widely.
Further rationale for decision to designate this clade can be found here: github.com/nextstrain/nco…
3/4
Based on sustained logistic growth in frequency in India, we've designed @PangoNetwork lineage BA.2.75 as clade 22D, labeled as "22D (Omicron)" to denote it still being considered as "Omicron variant" by @WHO. 1/4
Lineage BA.2.75 / clade 22D has been growing in frequency at a rate of 0.12 per day in India, which is equivalent to initial growth of BA.5 in the US and the UK, and is now outcompeting BA.5 in India. 2/4
These growth dynamics, along with mutational profile, strongly suggest this clade will spread widely, though it may not ultimately displace BA.5 viruses globally. Further rationale for decision to designate this clade can be found here: github.com/nextstrain/nco… 3/4