Another XBB.1.5* with S:456L, 90 seqs at 2023-05-03

[krosa1910]

Not Clear Sub-lineage pattern within xbb.1.5*, so I would propose as of now it is just a descendent of the total family
Defining Mutations: xbb.1.5*-〉Orf1a:S2822P/T8729C -〉+S:F456L/T22928C
Gisaid Inquiry: using the two defining mutation plus any restriction to xbb.1.5 or uploaded after 2023-Jan suffices

Lineage Collection: EPI_ISL_16978334, EPI_ISL_17007938, EPI_ISL_17017398,
EPI_ISL_17164892, EPI_ISL_17184221, EPI_ISL_17208855,
EPI_ISL_17232441, EPI_ISL_17232446, EPI_ISL_17241909,
EPI_ISL_17241934, EPI_ISL_17241943, EPI_ISL_17241964,
EPI_ISL_17241988, EPI_ISL_17242062, EPI_ISL_17242072,
EPI_ISL_17242092, EPI_ISL_17242112, EPI_ISL_17245727,
EPI_ISL_17245786, EPI_ISL_17245955, EPI_ISL_17284249,
EPI_ISL_17284252, EPI_ISL_17284260, EPI_ISL_17284455-17284456,
EPI_ISL_17284462, EPI_ISL_17284466, EPI_ISL_17296734,
EPI_ISL_17298943-17298944, EPI_ISL_17299126, EPI_ISL_17299141,
EPI_ISL_17363149, EPI_ISL_17363304, EPI_ISL_17363414,
EPI_ISL_17364077, EPI_ISL_17372888, EPI_ISL_17372968,
EPI_ISL_17373567, EPI_ISL_17409751, EPI_ISL_17418237,
EPI_ISL_17426624, EPI_ISL_17428866, EPI_ISL_17446707,
EPI_ISL_17470298, EPI_ISL_17470323, EPI_ISL_17470517,
EPI_ISL_17470622, EPI_ISL_17484889, EPI_ISL_17484892,
EPI_ISL_17485097, EPI_ISL_17525559, EPI_ISL_17526203,
EPI_ISL_17526798, EPI_ISL_17526894

Earliest Sequence: EPI_ISL_17007938, England 2023-02-06
Latest Sequence: EPI_ISL_17526894, Texas, US 2023-04-10
Distribution: 2 Austria, 46 England, 1 Netherland, 1 Germany, 1 Spain, 4 US (1 CA, 2NY, 1 TX)
After checking Yunlong Cao's twitter upon possible immune escape boost by S:456L, I decided to search upon it. Besides trees that are known to me (FD.1.1,FE.1,XBB.1.5.10), I discovered three new trees.
https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/singleSubtreeAuspice_genome_1b5a5_6081b0.json?f_userOrOld=uploaded%20sample (Large Tree, used to infer the structure)

The most interesting one being the green one was a sublineage of XBB.1.9.2, and although I did not found an issue with it, I though that it was possibly the recently designated EG.5. However, I may propose it to be enlarged in a later issue.
The pink and blue trees, however, seem undesignated. The pink one is boring because it is solely developed in England, and I learned not to trust England sequence numbers. Yet the blue one seems more interesting, as it shows some spread.
Thus, I would like to propose the blue tree defined by S:456L and Orf1a:S2822P
https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_334dc_68d620.json?f_userOrOld=uploaded%20sample

[krosa1910]

Not directly Related to this proposal, but I just realized that I mistakenly categorize a polyphyletic group into one (the green one). Instead of acquiring the common T22928C as in other trees, the upper branch of green group acquired T22930A, while the bottom branch acquired the regular T22928C. This is interesting.

[FedeGueli]

Hi @krosa1910 could you add the usher tree link to your proposal please?

[krosa1910]

Hi @krosa1910 could you add the usher tree link to your proposal please?

FIxed ( I was very tired and forgot to edit it in the standard way last night).

[FedeGueli]

thz no worries.

[krosa1910]

summary now: 2 Austria (no change), 49 England (+3), 1 Finland (New, detected 04-03, submitted today), no change for 1 each Nethenland, Germany, Spain , 1 Singapore (New, detected 04-14, submitted today), 7US (1 CA, 1 TX no change, 5 NY +3 with similar detection parameter)

[krosa1910]

It is really contradictory when I tried to do some growth analysis of this.
On one hand, the England origins are declining, this lineage ended with last 2 seqs at 04-04, three weeks from now. The weird peak around early March seem to decay a lot. Not very sure why, maybe is a fact from sequence patterns in England.
On another hand, the overseas spread is very successful. 13 seqs in 6 countries is not bad, and 6 of them lies in the last 15 days, which has just 5000 seqs in the whole Gisaid genome. US seem to be a new hotspot of it.
Judging from the genome itself for explanation, well there is no obvious successful trees. It just seem a broad, diverse collection of everything.

[krosa1910]

3 new sequences uploaded today, 1 england (but still earlier than the "ending time"), 1 france and 1 austria.
I suppose it is really something outside england, just ignore the island country origin may help us analyze its growth better.

[krosa1910]

recent spread to scotland and South Korea, 2 each

[krosa1910]

+3, 2 England, finally passing the "04-04 barrier" and one updated yesterday in Spain that I did not catch.

[FedeGueli]

@krosa1910 just spotted another XBB.1.5N:S194PS:F456L(T22928C) from Spain N_S194P, Spike_F456L it is something like 3% of spanish samples after 10th April likely just a cluster: https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_24d06_d0e730.json?c=country&label=id:node_5902649

[krosa1910]

@krosa1910 just spotted another XBB.1.5_N:S194P_S:F456L(T22928C) from Spain N_S194P, Spike_F456L it is something like 3% of spanish samples after 10th April likely just a cluster: https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_24d06_d0e730.json?c=country&label=id:node_5902649

This is very interesting, however, this one lacks 17124C, so I doubt it being part of XBB.1.5( although it seemed that cornelius still kept T17124C out of XBB.1.5 definition)

[krosa1910]

also get to switzerland, so +2 for total number to be 75 now. I guess it is good at spreading to foreign countries.