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sars-cov-2-variants / lineage-proposals

Repository to propose and discuss lineages
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KP.3 + S:N417T, ORF1a:D2492N, I3108V, ORF1b:Q48R + T177C [5' UTR] (26 seq, Canada, June 24) #1580

Closed ryhisner closed 3 months ago

ryhisner commented 5 months ago

Description Sub-lineage of: KP.3 Earliest sequence: 2024-5-5, Canada, British Columbia — EPI_ISL_19161088 Most recent sequence: 2024-5-11, Canada, BC — EPI_ISL_19169116, EPI_ISL_19169126 Continents circulating: North America (7) Countries circulating: Canada (7) [British Columbia (6), Alberta (1)] Number of Sequences: 7 GISAID Nucleotide Query: A22812C, A13610G CovSpectrum Query: Nextcladepangolineage:KP.3* & A22812C & [2-of: T177C, G7739A, A9587G, A13610G] Substitutions on top of KP.3: Spike: N417T ORF1a: D2492N, I3108V ORF1b: Q48R Nucleotide: T177C, G7739A, A9587G, C11644T, A13610G, A22812C

Phylogenetic Order of Mutations: C11644T → T177C, A9587G, A13610G, (ORF1a:I3108V, ORF1b:Q48R) → G7739A, A22812C (ORF1a:D2492N, S:N417T) → () → () →

USHER Tree https://nextstrain.org/fetch/raw.githubusercontent.com/ryhisner/jsons2/main/KP.3_N417T_7_seq.json?c=gt-S_417&gmax=25384&gmin=21563&label=id:node_6995166

image

Evidence Now in two Canadian provinces, British Columbia (6) and Alberta (1). All collection dates within 6 days of one another, from May 5-11. Upload dates all between May 23-28.

S:417T is one of the two most classic cryptic wastewater lineage mutations and is also quite common in conventional chronic-infection sequences, the other being ORF1a:K1795Q. Both also famously in Gamma.

The Alberta sequence also has ORF1a:T319S—a rare C->G nuc mutation—and N:G243C, which likely forms a disulfide bond in the predominant N dimer form.

Genomes

Genomes EPI_ISL_19161088, EPI_ISL_19163268, EPI_ISL_19169013, EPI_ISL_19169035, EPI_ISL_19169064, EPI_ISL_19169116, EPI_ISL_19169126
FedeGueli commented 5 months ago

+1 Alberta

ryhisner commented 5 months ago

+1 Alberta

The fact that the new Alberta sequence is identical to six sequences from British Columbia makes me think this could be spreading rapidly. Canada is quicker than the US (and just about all other countries) at uploading sequences, so I would not be surprised to see sequences of this showing up in the US in the next two weeks.

FedeGueli commented 4 months ago

26 all from Canada BC

FedeGueli commented 3 months ago

likely just a clustwer closing it