KP.1.1.3 + S:∆S31, S:T572I, ORF8:A65V (Full Quad) [32 sequences, 10 countries)

ryhisner commented 2 months ago

Description Sub-lineage of: KP.1.1.3 (S:R346T, F456L, K1086R, V1104L) Earliest sequence: 2024-5-21 – Spain, Catalunya Most recent sequence: 2024-6-3 – Canada, Ontario (2 seq) Continents circulating: North America (2), Europe (1) Countries circulating: Canada (2), Spain (1) Number of Sequences: 3 GISAID Nucleotide Query: G12160A, C29762T ,C23277T, C28087T CovSpectrum Query: Nextcladepangolineage: Substitutions/Deletions on top of KP.1.1.3: Spike: ∆S31, T572I ORF8: A65V 3' UTR: C29762T

Nucleotide: G12160A, ∆22193-22195, C23277T, C28087T, C29762T

USHER Tree https://nextstrain.org/fetch/raw.githubusercontent.com/ryhisner/jsons2/main/KP.1.1.3_Full_Quad.json?c=gt-nuc_12160&gmax=13060&gmin=11060&label=id:node_2376593

Evidence Collection date for Spain sequence is May 21 and for the two Canadian sequences June 3, so very recent. We haven't seen anything with all four known advantageous spike mutations (∆S31, R346T, F456L, T572I) take off though, so it may be that they don't work all that well together.

Logically, it seems like they should: S:T572I is known to increase ACE2 binding by increasing the 1-RBD-up conformation. This comes at the expense of antibody evasion since the RBD is more exposed, but one would expect T572I to be most tolerated on the most highly evasive RBDs, most notably sequences such as these that have the three major antibody-escape mutations. You would also expect S:T572I to go well with S:Q493E, particularly when joined with S:∆S31 (or maybe S:S31F).

Genomes

Genomes

EPI_ISL_19165019, EPI_ISL_19188373, EPI_ISL_19188377

FedeGueli commented 2 months ago

One more sample from Canary Island , but @angiehinrichs i m noticing that USher changes placement frequently , sometimes from night to morning, now it is placed as KP.1.2 sublineage (and it is a misplacement cause having C4999T and S:S31del for sure it belongs top KP.1.1.3 ) @ryhisner i suggest this as query: G12160A, C29762T ,C23277T, C28087T

tree: