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sars-cov-2-variants / lineage-proposals

Repository to propose and discuss lineages
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KS.1 + S:V642A (56) 6-7% in Dominican Republic #1535

Closed FedeGueli closed 2 months ago

FedeGueli commented 5 months ago

KS.1 > S:V642A ( T23487C)

Query: T22928C, G24821T,T23487C

Samples : 5 on Gisaid 7 on Usher

EPI_ISL_19019160, EPI_ISL_19019188, EPI_ISL_19019200, EPI_ISL_19054256, EPI_ISL_19070085

Tree:

Screenshot 2024-04-26 alle 10 26 19

https://nextstrain.org/fetch/genome-test.gi.ucsc.edu/trash/ct/subtreeAuspice6_genome_test_471cf_abe240.json?c=userOrOld&label=id:node_7036547

ryhisner commented 5 months ago

This is on the opposite side of the 630 loop from P621S. S:V642G is more common, but I'm guessing V642A has a similar effect. BA.2.87.1 had/has both P621S and V642G. P621S definitely makes the RBD-up conformation more common. I'm not sure what V642G does though.

FedeGueli commented 5 months ago

Thank you Ryan!

FedeGueli commented 5 months ago

luckily it seems slow

FedeGueli commented 4 months ago

8 slow.closed

FedeGueli commented 3 months ago

This one is back with many samples uploaded in June from Dominican Republic and via GBW from Dominican republic and Panama New Tree:

Screenshot 2024-06-25 alle 23 02 00

https://nextstrain.org/fetch/genome-test.gi.ucsc.edu/trash/ct/subtreeAuspice11_genome_test_20ceb_b11020.json?label=id:node_7150966

Estimated prevalence in Rep. Dominicana is around 7% after May 15

FedeGueli commented 3 months ago

@corneliusroemer ping

FedeGueli commented 3 months ago

25 +3 Japan via GBW

FedeGueli commented 3 months ago

54 it entered a long term care facility cluster in Ontario

FedeGueli commented 2 months ago

Designated KS.1.3 via https://github.com/cov-lineages/pango-designation/commit/ea75ab8e923e0e05ae7a94fa70c3c4172d2bd50b