XBB.1.22.1 sublineages with S:K478R emerged in Indonesia (70 seqs)

[HynnSpylor]

Defining mutations: XBB.1.22.1>A22995G (S:K478R)
GISAID query: Spike_Y200C, Spike_T478R, Spike_F486P, -G5720A (to exclude some XBB.1.9 samples)
Earliest seq: 2023-03-10 (Indonesia, EPI_ISL_17324407)
Most recent seq: 2023-04-12 (China- Hubei Province, EPI_ISL_17545712)
Countries detected: Indonesia (3), China (2), South Korea (1)

Usher Tree:

https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_1774_937500.json

S:K478R is very popular recently as the fast growing of XBB.1.16, but recently many other XBB.1*+F486P lineages gradually emerge it, maybe it will become more convergent.
Now the XBB.1.22.1+S:K478R is only 6 seqs. But notice that the latest two seqs (actually at least 3 seqs by GenBase) locates in Central China with high density of population (the total population of Hubei and Henan is more than 150M). As the other XBB.1.22.1 sublineage is spread in Hubei and Henan province (the red points in the figure below), the growth potential is of concern and worth monitoring.

Genomes:
EPI_ISL_17324407, EPI_ISL_17469963, EPI_ISL_17470013, EPI_ISL_17511611, EPI_ISL_17545706, EPI_ISL_17545712,

[GeorgeS2019]

@HynnSpylor
I have reason to believe from the protein structure of spike that S:K478R of e.g. XBB.1.16 could enhance RBD binding that is absent in e.g. S:T478K e.g. XBB.1.5

Please suggest where I could track this mutation more effectively.

[HynnSpylor]

@GeorgeS2019 Welcome to the community! I suppose that prompt attention to tracking the update of genome databases (GISAID, GenBase, etc., personal account is required) is enough. Welcome to open an issue and discuss if you find some new sublineages, it will be more effective.

[aviczhl2]

actually at least 3 seqs by GenBase

How to do mutation-specific query on GenBase, and what are those seqs' IDs? Usher updates Genbase seqs daily now so they shall be on usher tree. Is the other one placed elsewhere?

[corneliusroemer]

There are really 2 lineages here:
One detected in US with one travel surveillance suggesting it's from India, 4 seqs, with A19134G, C25836T on branch [this is now sublineage of FY.1]
The other one in Indonesia, China, South Korea with 6 seqs, directly on polytomy it seems,

Both are small, so let's see how things develop before designating. Ping me as soon as one reaches 20 sequences, until then let's just watch - too many comments make things hard to review.

[corneliusroemer]

@Memorablea it would be very helpful if you added quantitative statements for growth (e.g. how many sequences now per cluster) and new Usher pics. That makes it much more valuable to everyone. As is your comment is noise and not much info

[HynnSpylor]

@aviczhl2 Nowadays the seqs in China have been continued to update in GISAID. So the problem has been solved.
Back on topic, there are no new seqs these days (in GISAID). We should keep on monitoring for a time.

[GeorgeS2019]

I have reasons to believe that XBB.1.16 will prevail in the US, replacing all growth advantage gained by XBB.1.9.1 over XBB.1.5

What will be critical will be WHICH will replace XBB.1.16

From which country WILL this successor of XBB.1.16 will come from

Am I assuming right, this could be XBB.1.122.1?

[FedeGueli]

I have reasons to believe that XBB.1.16 will prevail in the US, replacing all growth advantage gained by XBB.1.9.1 over XBB.1.5

What will be critical will be WHICH will replace XBB.1.16

From which country WILL this successor of XBB.1.16 will come from

Am I assuming right, this could be XBB.1.122.1?

Hi feel free to open up a discussion issue in the new low priority page you find the link in the pinned issue in the homepage.

That kind of consideration can be widely disccussed there.

[Memorablea]

@Memorablea it would be very helpful if you added quantitative statements for growth (e.g. how many sequences now per cluster) and new Usher pics. That makes it much more valuable to everyone. As is your comment is noise and not much info

I found two sequences on GenBase, namely C_ AA011613.1 and C_ AA011612.1

[HynnSpylor]

@Memorablea Nowadays the sublineage with ORF1a:E750K has been designated as FY.3 (and it is the main branch of XBB.1.22.1 in China). But the S:S408R is a reversed mutation and quite likely artefacts.
The 2 new S:K478R seqs were updated several days ago, Thx for updating the Usher. But the seqs are not further increased these days. We should monitor for a time.

https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_2e5fe_5b6830.json?c=gt-S_478&label=id:node_5892381

[HynnSpylor]

Today Indonesia updated 10 seqs on branch A (in Indonesia, China, South Korea and Japan), and the total is 24 (duplicate seqs are excluded).

[HynnSpylor]

Now the branch A reaches 56 samples, and it has notably spread in Indonesia.
@corneliusroemer I suggest it could be designated.

https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_221a1_8443b0.json

Now Branch B is a branch of FY.1, 14seqs with relatively low growth rate

[FedeGueli]

@HynnSpylor pls update the headline!

@corneliusroemer def one to get designated at first glance looking the xbb.1.22.1 tree:

[FedeGueli]

Now 89 seqs in XBB.1.22.1 with S:T478R please @corneliusroemer designate the main branch:

https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_1818e_4c42f0.json?f_userOrOld=uploaded%20sample&label=id:node_6638434

cc @HynnSpylor remove lineage B from this issue and propose it separately please casue we cna track both better. this one deserves rapid designation.

[FedeGueli]

Lineage B is :
https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_1818e_4c42f0.json?c=gt-S_478&label=id:node_6637654

Defining FY.1 > S:T478R
Gisaid query: G18811A,A24813G
Sequences : 8

[HynnSpylor]

Now I change the title and focus on the former "Branch A"
I'll put Branch B (FY.1 sublineage) in SARS-Cov-2 lineage proposals for tracking

[FedeGueli]

Thx @HynnSpylor !

[HynnSpylor]

2 more seqs from Netherlands