XBB.1.9.1 sublineage with S:D215V (A22206T) rapidly increases in China (169 seqs)

[HynnSpylor]

*Transferred from sars-cov-2-variants/lineage-proposals#62

Defining mutations: XBB.1.9.1>C3511T>A22206T(S:D215V)
GISAID query: Spike_D215V, C3511T, C11956T
Earliest seq: 2023-04-25 (Sichuan Province, China, EPI_ISL_17637501)
Most recent seq: 2023-05-08 (Hubei Province, China, EPI_ISL_17671943)
Countries detected: China (57, Hubei Province 27, Sichuan Province 21, Shanghai Municipality 6, Gansu Province 1, Henan Province 1, Heilongjiang Province 1)

Usher Tree:

https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_3059b_77bd80.json
A very new sublineage in China, and it grows rapidly and distributes widely- Heilongjiang is in northeastern China while Sichuan in southwestern China.

Nowadays XBB.1.9.1 is the dominant sublineage in China, and the sublineage should be highly concerned.

Genomes:
EPI_ISL_17625358, EPI_ISL_17625461, EPI_ISL_17625620, EPI_ISL_17637501, EPI_ISL_17645399, EPI_ISL_17645402, EPI_ISL_17645453, EPI_ISL_17645470, EPI_ISL_17645642, EPI_ISL_17652398, EPI_ISL_17664522, EPI_ISL_17664524, EPI_ISL_17664544, EPI_ISL_17664547, EPI_ISL_17664551, EPI_ISL_17664570, EPI_ISL_17671912, EPI_ISL_17671940, EPI_ISL_17671943, EPI_ISL_17671958, EPI_ISL_17671980,
EPI_ISL_17672057, EPI_ISL_17678295, EPI_ISL_17678310, EPI_ISL_17678340, EPI_ISL_17678402, EPI_ISL_17683972, EPI_ISL_17683976, EPI_ISL_17684009, EPI_ISL_17684015, EPI_ISL_17684045, EPI_ISL_17684066, EPI_ISL_17684088, EPI_ISL_17684096, EPI_ISL_17684120, EPI_ISL_17684125, EPI_ISL_17684135, EPI_ISL_17684140-17684141, EPI_ISL_17684150, EPI_ISL_17684152, EPI_ISL_17684161, EPI_ISL_17684192-17684193, EPI_ISL_17684202, EPI_ISL_17684326, EPI_ISL_17684417, EPI_ISL_17684423, EPI_ISL_17684425, EPI_ISL_17684431-17684434, EPI_ISL_17684437-17684438, EPI_ISL_17684443, EPI_ISL_17684467,

[HynnSpylor]

2 more seqs from Singapore. Notice that one is local case, and another with travel history to USA

[xz-keg]

Worth noting that currently top 5 fastest lineages on collection42 https://cov-spectrum.org/collections/42 are all Chinese variants.

[FedeGueli]

@aviczhl2 to me that reflects recency of sequences uploaded. China has shortened time from collection to upload and increased its global share of genomes uploaded to Gisaid.
Not sure this explains everything maybe just one factor of many

[xz-keg]

@aviczhl2 to me that reflects recency of sequences uploaded. China has shortened time from collection to upload and increased its global share of genomes uploaded to Gisaid. Not sure this explains everything maybe just one factor of many

Yeah among those variants only EG.5.1 shows a global advantage.

[FedeGueli]

@aviczhl2 to me that reflects recency of sequences uploaded. China has shortened time from collection to upload and increased its global share of genomes uploaded to Gisaid. Not sure this explains everything maybe just one factor of many

Yeah among those variants only EG.5.1 shows a global advantage.

Yeah but this one seems very fast look at last weeks of may:

cc @InfrPopGen @corneliusroemer looking at Chinese data only on Covspectrum (reliable cause they have cut timing from sampling to uploading) this seems quite doubling every week
https://cov-spectrum.org/explore/China/AllSamples/from%3D2023-05-01%26to%3D2023-05-30/variants?aaMutations1=S%3A153I%2CS%3A1258Q%2CN%3A151L&

[HynnSpylor]

113 seqs now. In addition, South Korea updated 12 seqs with Spike mutation only. It seems like XBB.1.9.1+S:D215V but can not be confirmed.

[xz-keg]

Yeah but this one seems very fast look at last weeks of may:

I guess this may partially due to provincial uploading issues. Different provinces of China upload differently, and when some increases their sequences the provincial local dominated variants start to have a false advantage.

Unfortunately cov-spectrum cannot do province-level growth analysis, can it?

[FedeGueli]

No it can on the growth advantage tool show more button

[xz-keg]

No it can on the growth advantage tool show more button

Yeah. This one do have a quite high relative advantage against its parent XBB.1.9.1 in provincial level. Thanks.

[xz-keg]

169 seqs now.