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cov-lineages / pango-designation

Repository for suggesting new lineages that should be added to the current scheme
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Similar to EG.5.1: xbb.1.9.1 with s:456l and s:52h (25 seqs). Interesting: 2 seqs with s:455W #2072

Closed BorisUitham closed 1 year ago

BorisUitham commented 1 year ago

Query: G21718C, T22928C, C25714T Collected: 2023-04-29 and 2023-05-12

I tracked this since 2 seqs because this is pretty much the xbb.1.9.1 equivalent of xbb.1.9.2's eg.5.1 which does have a large growth advantage. And i did expect it to grow similarly. Seems like a month later it has indeed grown from 2 to 19 sequences with wide spread. 2 sequences from england have the combination s:455w s:456l, which has happened before in chronics, but not yet in a lineage that actually has capability to spread so it is very important to keep an eye on that. Spikes are identical to eg.5.1, the difference is in a lot of the nucleotides before the spike. If you compare presence of accessory mutations, the difference with eg.5.1 is that this has: Orf3a:L108F Orf1a:I2010V S:455W (in 2 english sequences)

And eg.5.1* has Orf1a:a690v Orf1a:a3413v Orf1b:d54n (in eg.5.1.1)

Lots of doubles in this screenshot, but that was necessary because 1 of the 2 455w english sequences is not on gisaid: Screenshot_20230628_013628_Chrome

https://nextstrain.org/fetch/genome-test.gi.ucsc.edu/trash/ct/subtreeAuspice1_genome_test_59e95_b71ba0.json

https://cov-spectrum.org/explore/World/AllSamples/Past6M/variants?nucMutations=G21718C%2CT22928C%2CC25714T&

BorisUitham commented 1 year ago

For more in depth discussion also a out 455w 456l check: https://github.com/sars-cov-2-variants/lineage-proposals/issues/95

Thank you @oobb45729 and @tylernstarr

BorisUitham commented 1 year ago

There is a 242-243 del in one of the spanish sequences. Dunno if its an artifact. But it is a hallmark of xbc and b.1.351 lineages

BorisUitham commented 1 year ago

3 more sequences, but 1 is yet another 455w from england!

Edit: false alarm. It is just that one finally being uploaded to gisaid: usher now shows 5 different sequences but only 2 are unique. I guess its 2 gisaid, 2 cog-uk and 1 genbank Screenshot_20230629_182919_Chrome

FedeGueli commented 1 year ago

cc @corneliusroemer @thomaspeacock @InfrPopGen i suggest a rapid review of this one.

corneliusroemer commented 1 year ago

First thought this might be a recombinant of EG.5.1, but nope, both EG.5.1 aa mutations have different underlying nucs (22928 vs 22930 etc)

BorisUitham commented 1 year ago

@corneliusroemer even the cause of s:52h is different; (G21718C) in fl.20 vs (G21718T) in eg.5.1!

HynnSpylor commented 1 year ago

one more seq (from US International Airport with UK travel history) get S:L455W I suggest it should be a further watch

FedeGueli commented 1 year ago

one more seq (from US International Airport with UK travel history) get S:L455W I suggest it should be a further watch

@BorisUitham will propose it as soon as possible

FedeGueli commented 1 year ago

proposed : https://github.com/sars-cov-2-variants/lineage-proposals/issues/295