Designate 4 new clades: CH.1.1 -> 23C, XBB.1.9 -> 23D, XBB.2.3 -> 23E, EG.5.1 (XBB.1.9.2.5.1) -> 23F

[corneliusroemer]

With this PR, we are designating 4 new Nextstrain clades:

• 23C = CH.1.1 (= BM.4.1.1.1 = BA.2.75.3.4.1.1.1)
• 23D = XBB.1.9
• 23E = XBB.2.3
• 23F = EG.5.1 (XBB.1.9.2.5.1)

23C = CH.1.1 (= BM.4.1.1.1 = BA.2.75.3.4.1.1.1)

23C = CH.1.1 is a sublineage of 22D = BA.2.75 with extra Spike receptor binding domain mutations 346T, 444T, 452R and 486S. It is an important non-XBB lineage that has co-existed with XBB and is undergoing further antigenic evolution. It is currently most common globally in New Zealand and Australia (10-40%) but also present in Europe (1-10%).

23D = XBB.1.9

23D = XBB.1.9 is a major clade of XBB.1 characterized by ORF9b:I5T (shared with 23B = XBB.1.16), ORF1a:G1819S and ORF1a:T4175I. While it does not have 486P, the two main sub-lineages XBB.1.9.1 and XBB.1.9.2 both do. As XBB.1.9.1 and XBB.1.9.2 differ only by synonymous mutations, we designate their parent instead to minimize the number of clades. Globally, 23D = XBB.1.9 has overtaken 23A = XBB.1.5 roughly in May 2023 and is further rising. In July 2023, 23D accounted for around 1/3 of global sequences.

23E = XBB.2.3

23E = XBB.2.3 is the only major XBB clade with S:486P that is from the XBB.2 (S:D253G) branch of XBB instead of XBB.1 (S:G252V). XBB.2.3 has the additional Spike mutation S:521S and is the only XBB lineage with ORF1b:P959S, a reversion to the original genotype (the ORF1b:S959P mutation is the defining mutation of BA.2.10, XBB got it from its NTD donor BA.2.10.1). 23E has grown steadily since it first appeared in early 2023 and is now globally at around 10%. It is most common in South and South East Asia.

23F = EG.5.1 (= XBB.1.9.2.5.1)

23F = EG.5.1 is a subclade of 23D = XBB.1.9 with extra spike mutations 486P, F456L and Q52H. It has been growing steadily since it was first sequenced in March 2023 and represented around 20% of sequences at the end of July. 23F is particularly common in China, where it is about to become dominant. However, EG.5.1 is growing on all continents. It is the first Nextstrain clade with Spike RBD mutation S:F456L.

Subtree of XBB showing new Nextstrain clades 23D/E/F:

Subtree of BA.2 showing new clade 23C = CH.1.1

Pre-merge checklist

• ncov file updates:
  • defaults/clades.tsv
  • defaults/clade_emergence_dates.tsv
  • defaults/clade_hierarchy.tsv
  • defaults/clades_display_names.yml
  • defaults/color_ordering.tsv
  • defaults/emerging_lineages.tsv (if needed)
• Explain in PR why we are elevating
• Check trial builds: https://next.nextstrain.org/staging/ncov/open/trial/new-clades-2023-08/global/2m

Post merge checklist

• Add new variant (with new name) to Nextclade dataset
• Trigger full runs on GISAID & Genbank once Nextclade updated
• Update clade diagram figure
• Tweet about new variant

[trvrb]

Thank you @corneliusroemer for putting in the PR. I'm further documenting here the rationale behind why these particular lineages pass our clade designation criteria.

Lineage CH.1.1 / Clade 23C

This is less than 5% global frequency in the past 6M and never more than ~13% in Europe. However, in the all time Oceania build, we see CH.1.1 goes above 30% on Jan 15 and remains above 30% until July.

Oceania frequency

This matches our designation criteria that

3. A clade reaches >30% regional frequency for 2 or more months

Lineage XBB.1.9 / Clade 23D

As seen in the global all-time build lineage XBB.1.9 is currently at 21% global frequency and has been continuously above the 20% global frequency since May, so >3 months.

Global frequency

This matches our designation criteria that

2. A clade reaches >20% global frequency for 2 or more months

Lineage XBB.2.3 / Clade 23E

XBB.2.3 is under 6% global frequency and under 10% frequency in Asia. So doesn't meet broader frequency criteria.
However, there is a recent increase in India. CoV-Spectrum places it at 30-50% current frequency. In the 2m Asia build, it's at about 50% frequency in India.

Without specifically looking at India, XBB.2.3 doesn't meet our criteria. It's growing at between 0.00 and 0.03 per day across most countries.

However, in India, clade growth is faster at 0.12 per day and is now potentially well above 50%.

Thus, XBB.2.3 passes our criteria that

5. A clade shows consistent >0.10 per day growth in frequency in a country with at least 50M people and has reached >25% frequency within this country

Lineage EG.5.1 / Clade 23F

EG.5.1 has quickly overtaken parental EG.5* lineage, where recent EG.5*-derived viruses are basically all EG.5.1.

EG.5.1 is currently at 24% frequency in Asia according to 6m Asia build, so it doesn't meet the frequency threshold. However, EG.5.1 has been growing consistently in countries where its circulating that are reporting enough recent sequences to analyze:

Countries with data show Canada at 0.08 per day, China at 0.04, Japan at 0.05, Singapore at 0.06, South Korea at 0.05 and USA at 0.04. Thus, EG.5.1 has cleared the clade growth threshold.

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