Elevate lineage XDV.1 as clade 24D and lineage KP.3.1.1 as clade 23E

[trvrb]

With this PR, we are designating clades 24D (lineage XDV.1) and 24E (lineage KP.3.1.1).

Clade 24D, lineage XDV.1

Clade 24D, lineage XDV.1 stems from a rather complex recombination event. XDV is officially a recombinant of ["XDE","JN.1","XDE","JN.1"] and XDE is officially a recombinant of ["GW.5.1","FL.13.4"].

• JN.1 is clade 24A
• GW.5.1 belongs to clade 22F, ie lineage XBB
• FL.13.4 belongs to clade 23D, ie lineage XBB.1.9
• The naive phylogeny from https://nextstrain.org/ncov/gisaid/asia/all-time?c=Nextclade_pango groups XDV.1 as a sister clade to XBB just because BA.2.86 is a sister clade
• In terms of picking a single parent for the schematic I think the most reasonable choice is clade 21L / lineage BA.2, but could defer to other's opinions as this is the clade parent in the naive phylogeny

XDV.1 has become particularly prevalent in China where it's outcompeting JN.1-derived viruses:

From https://nextstrain.org/sars-cov-2/forecasts:

From https://cov-spectrum.org/explore/China/AllSamples/Past6M/variants?nextcladePangoLineage=XDV.1*:

In our "Asia" analysis, we're placing XDV.1 at ~30% over the past two months, slightly rising from 29% in late June to 32% in late Aug.

From https://nextstrain.org/ncov/gisaid/asia/2m?c=Nextclade_pango&f_region=Asia:

Although it's growth may have slowed relative to other circulating viruses in China, it's still quite prevalent:

Thus, 24D / XDV.1 fulfills our clade designation criteria 3: "A clade reaches >20% regional frequency"

Clade 24E, lineage KP.3.1.1

Clade 24E, lineage KP.3.1.1 stems from mutation accumulation on top of clade 23C (lineage KP.3). These mutations are synonymous nucleotide mutations G15372T and A19722G (KP.3 → KP.3.1) as well as synonymous nucleotide mutation C12616T and ORF1a amino acid mutation S4286C (via nucleotide mutation A13121T) and spike deletion at codon 31 (KP.3.1 → KP.3.1.1).

KP.3.1.1 showed a significant fitness increase over clade 23C (lineage KP.3) and is now quite common.

From https://nextstrain.org/sars-cov-2/forecasts:

From https://cov-spectrum.org/explore/World/AllSamples/Past6M/variants?nextcladePangoLineage=KP.3.1.1*:

In our "global" analysis, we're placing KP.3.1.1 at 14% rising to 24% over the past two months. From https://nextstrain.org/ncov/gisaid/global/2m?c=gt-nuc_13121:

In Europe, we're placing it at 51% rising to 64%. From https://nextstrain.org/ncov/gisaid/europe/2m?c=gt-nuc_13121&f_region=Europe:

Growth and current prevalence relative to existing clades in countries with sufficient data can be seen here:

Thus, 24E / KP.3.1.1 fulfills our clade designation criteria 3: "A clade reaches >20% regional frequency" as well as 4: "A clade shows consistent >0.05 per day growth in frequency where it's circulating and has reached >5% regional frequency". And it's about to cross to the threshold for criteria 2: "A clade reaches >20% global frequency for 2 or more months".

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)
• ncov-ingest file update: https://github.com/nextstrain/ncov-ingest/blob/master/defaults/clade-legacy-mapping.yml
• Explain in PR why we are elevating
• Check trial builds:
  • https://nextstrain.org/staging/ncov/gisaid/trial/clade-24D/global/2m
  • https://nextstrain.org/staging/ncov/gisaid/trial/clade-24D/asia/2m
• PR approval

Post merge checklist

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

[Huachuan1120]

I just learned from a friend that the naming rule is that as long as the branch accounts for more than 30% for more than two consecutive months, it can get a new number. So from this point of view, XDV.1* will just have the opportunity to get a new number, while Japan's XDQ* will not be able to get it due to lack of time. I apologize for directly proposing my ideas without fully understanding the naming rules. I was wrong and I apologize to everyone. However, we still need to pay attention to the monthly COVID-19 report released by the CDC in mainland China in early September. The trend of XDV.1* in mainland China reflected in the report will be very important.

[trvrb]

Trial builds look good to me. I believe this should be good to merge.

[trvrb]

Okay. I decided to go ahead and add clade 24E elevating lineage KP.3.1.1 to this PR. This lineage clearly meets our current criteria. By elevating these two clades at the same time, it will make for a bit less work in some of the downstream maintenance. Full justification for KP.3.1.1 is above.

Trial builds with both 23D 24D and 23E 24E are now running at https://github.com/nextstrain/ncov/actions/runs/10822261952.

[trvrb]

Trial builds like https://nextstrain.org/staging/ncov/gisaid/trial/clade-24D/global/2m look good. I'm going to plan to merge this in the next couple of days. cc @corneliusroemer @rneher @emmahodcroft

[Memorablea]

Okay. I decided to go ahead and add clade 24E elevating lineage KP.3.1.1 to this PR. This lineage clearly meets our current criteria. By elevating these two clades at the same time, it will make for a bit less work in some of the downstream maintenance. Full justification for KP.3.1.1 is above.

Trial builds with both 23D and 23E are now running at https://github.com/nextstrain/ncov/actions/runs/10822261952.

it is 24D and 24E.Please notice the text.

[corneliusroemer]

This is great, thanks @trvrb! Sorry for the delay in getting back on this - been super busy with Pathoplexus.

I'll merge this now so I can include it in the latest Nextclade build I'm preparing.

[trvrb]

Awesome! Thanks so much @corneliusroemer.

[xz-keg]

Does XEC already satisfy criteria 4 now? I see it is 5%/day growth over KP.3.1.1(and more against general variants) and now ~10% in Europe.

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