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sars-cov-2-variants / lineage-proposals

Repository to propose and discuss lineages
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KP.2.3 + S:K478T (Rev) (110) #1834

Closed FedeGueli closed 3 months ago

FedeGueli commented 3 months ago

There seems to be a trend in reverting 478K to T in KP.2.3 , Usher actually put three branches together i m a bit skeptical they are one only one lineages. But being mostly GBW samples from India and Middle East , where KP.2 FLiRT emerged first, i think it is worth tracking them. Obviously to find a query with a reversion is a very hard job so i will set a general query toi catch all KP.2.3 + 478T sequences, plus three queries specific for the three main branches of the tree. Query for all KP.2.3+ 478T: del21653, C22000A,G25593T, -22995A,-22995T,-22995G, C28714T Samples: 110 Query for Kp.2.3+ 478T>C28714T: del21653, C22000A,G25593T, -22995A,-22995T,-22995G, C28714T Samples: 78 Query for Kp.2.3+ 478T>C2232T: C2232T,del21653, C22000A,G25593T, -22995A Samples: 5 Query for Kp.2.3+ 478T>C4296T : del21653, C22000A,G25593T, -22995A

Apparent tree:

Screenshot 2024-08-05 alle 12 06 59 Screenshot 2024-08-05 alle 12 07 11

https://nextstrain.org/fetch/genome-test.gi.ucsc.edu/trash/ct/singleSubtreeAuspice_genome_test_9f8f_1e10.json?c=gt-S_478&f_userOrOld=uploaded%20sample&gmax=25384&gmin=21563&label=id:node_7055844

xz-keg commented 3 months ago

How can we query exactly for seqs with 22995 being C on gisaid (not missing coverage)?

FedeGueli commented 3 months ago

How can we query exactly for seqs with 22995 being C on gisaid (not missing coverage)?

i m still trying to get that.

FedeGueli commented 3 months ago

How can we query exactly for seqs with 22995 being C on gisaid (not missing coverage)?

it should be -Spike_T478 8nextclading then for count manually the NNN and exclude them)

xz-keg commented 3 months ago

How can we query exactly for seqs with 22995 being C on gisaid (not missing coverage)?

it should be -Spike_T478 8nextclading then for count manually the NNN and exclude them)

Query on cov-spectrum with S:478T, it has a few days delay.

FedeGueli commented 3 months ago

Not useful, just now the trend toward 478rev is clear for many lineages.

xz-keg commented 2 months ago

Total 289 while lineage on C28714T branch now totals 205.

Most of them seems to be simply missing coverage issues, however, there really exists some with real reversions.

xz-keg commented 3 weeks ago

designated KP.2.3.10 via https://github.com/cov-lineages/pango-designation/commit/b2f9b67175ca250de1589e84cfc82c9cc6020c85