XBB.1.19.1 with ORF1a:S302F, ORF1a:P2079Q, ORF1a:P4220L, S:L455F, S:F456L, S:K478I, N:P80S (5 seq. China ex UAE, Australia, Canada, US)

[oobb45729]

EDITED

Defining mutations: XBB.1.19.1 (S:E554K) : > N:P80S (C28511T) > Orf1a:S302F (C1170T) > Orf1a:P2079Q (C6501A), C12473T, Orf1a:P4220L(C12924T), S:K478I (A22995T), C24034T, T24046C, T28723C > S:L455F (G22927T), S:F456L (T22928C) Query : T28723C,G22927T,T22928C,C12473T (Edited) Tree: https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_1a7fa_fc5a90.json?label=id:node_6625137

Samples: hCoV-19/Canada/ON-PHL-23-26905/2023|EPI_ISL_18030523|2023-07-15 hCoV-19/USA/NJ-CDC-QDX82431222/2023|EPI_ISL_18022751|2023-07-05 USA/NY-PRL-230711_81B06/2023|OR342426.1|2023-07-08 hCoV-19/Australia/WA14482/2023|EPI_ISL_17999822|2023-07-07 hCoV-19/Shanghai/SCDC-HG0504-476/2023|EPI_ISL_17645716|2023-05-01

---

ORIGINAL ISSUE: C_AA014164 or/and EPI_ISL_17645716 (I don't know whether they are the same or not).

https://cov-spectrum.org/explore/China/AllSamples/Past6M/variants?variantQuery=S%3A455F%26S%3A456L%26S%3A478I& https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_41985_2764a0.json?c=gt-S_455&label=id:node_6687574

edited: Spike_T478I,Spike_L455F

[FedeGueli]

Thanks for highlighting, here it is possible to highlight also singlets , i ask just the kindness of track them in the first two weeks after the first "proposal" if no new sequence has come into the game please close this kind of issue by yourself.

So for this one i fix closing date for 1st of June if no sequence has been uploaded before.

Ok?

[oobb45729]

No problem.

[oobb45729]

Considering how relatively new XBB.1.19.1 is in China, this strain likely did not originate in China. I wonder where it comes from.

[xz-keg]

Considering how relatively new XBB.1.19.1 is in China, this strain likely did not originate in China. I wonder where it comes from.

XBB* has been circulating in China for a very long time, it is just not sequenced due to CCDC's low sequencing density.

Especially in some areas like Beijing, where zero sequences have been uploaded in the recent month.

We already have long Chinese XBB saltations like https://github.com/sars-cov-2-variants/lineage-proposals/issues/16

[oobb45729]

https://ngdc.cncb.ac.cn/genbase/search/gb/C_AA014164.1?lang=en So it's from UAE, where no sequences was uploaded recently.

[HynnSpylor]

Now Australia updated another sample without ORF1a:H1160Y and N:T379I

[FedeGueli]

New query: Spike_T478I,Spike_L455F

[FedeGueli]

Two more sequences of this one one from New Jersey and another from Canada. Please propose it @oobb45729

[FedeGueli]

Another one from NYC not yet on Gisaid 5 in total. Ping @corneliusroemer i suggest direct designation of this one first time we see 455-456-554

[FedeGueli]

Designated GW.5 via https://github.com/cov-lineages/pango-designation/commit/166dd7494a8bf79105a7e58a54449813863dd044