search

sars-cov-2-variants / lineage-proposals

Repository to propose and discuss lineages
42 stars 1 forks source link

Other KP.3 sublineages with S:S31del #1700

Open JosetteSchoenma opened 4 days ago

JosetteSchoenma commented 4 days ago

While searching for KP.3.1.1. samples that might be missed due to missing coverage, I found some probable convergent KP.3 sublineages with S:S31del. I used the query: Spike_S31del, Spike_Q493E, -A13121T, -G22111T

-A13121T to exclude KP.3.1.1 found by the nuc query. -G22111T to exclude XDY.

Usher, top branches are probably (partly) KP.3.1.1 with some missing coverage. image

@FedeGueli helped me to look at the branches and found queries for them. Thank you!

KP.3.3.1 with extra S:A163V 2 samples from USA/California airport screening. 1 from Taiwan, other probably pooled Query: C22050T, C2668T, T3565C

KP.3.2.4 singlet with extra S:S155I Query: T22292C, A28984G, del21653 1 Canada/Ontario

KP.3.2 singlet Western Australia Query: T28952C, del21653

KP.3.3 singlet England Query: G1836A , C18744T, del21653

FedeGueli commented 4 days ago

Thank you @JosetteSchoenma great spot!! This could be a game changer if these singlets will turn out to be growing it would mean that soon we will see fireworks with even more fit lineages than KP.3.1.1. Especially the KP.3.3.1 + 31del is one to watch: already a fast lineage ( the only one competing with KP.3.1.1 according to Collection 42 with 3 spike mutations over vanilla KP.3 (31del,163V 547K) , emerging in an undersampled area ( or better saying a slow in uploading area) and already found via GBW airport surveillance so hinting at some sort of prevalence in the region where it emerged. Ping @corneliusroemer i will keep you updated on all these convergent lineages and especially if more KP.3.3.1-31del wil pop up