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Repository for suggesting new lineages that should be added to the current scheme
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KP.3.1.6 + S:R346T, H445R; ORF1a:L293F, S1272G, T2069N, D2592Y (>20 seq; Aug 6) #2699

Closed ryhisner closed 1 month ago

ryhisner commented 1 month ago

Description (Transferred from https://github.com/sars-cov-2-variants/lineage-proposals/issues/1655)

Sub-lineage of: KP.3.1 Earliest sequence: 2024-6-8, USA, Colorado – EPI_ISL_19217715, EPI_ISL_19217894 Most recent sequence: 2024-7-9, USA, Iowa - EPI_ISL_19284825 and USA, New York - EPI_ISL_19277632 Continents circulating: North America (10), Asia (2) Countries circulating: USA (10), Japan (1), United Arab Emirates (1) Number of Sequences: 12 GISAID Nucleotide Query: C6471A, G22599C, G22895C, T22896G CovSpectrum Query: Nextcladepangolineage:KP.3.1* & [2-of: G22599C, A22896G] Substitutions on top of KP.3.1: Spike: R346T, H445R ORF1a: L293F, S1272G, T2069N, D2592Y Nucleotide: C1142T, A4079G, C6471A, A7432G, G8039T, T19305C, G22599C, A22896G

Phylogenetic Order of Mutations: T19305C → G8039T (ORF1a:D2592Y) → A4079G (ORF1a:S1272G) → C1142T (ORF1a:L293F) → C6471A, A7432G, G22599C, A22896G (S:R346T, S:H445R, ORF1a:T2069N)

USHER Tree https://nextstrain.org/fetch/raw.githubusercontent.com/ryhisner/jsons2/main/KP.3.1_v445r_r346t.json?c=gt-S_445&gmax=25384&gmin=21563&label=id:node_7003604

image

Evidence These are just the 3rd and 4th KP.3 sequences with S:R346T, and they are the first with evidence of transmission. Clearly, there is something about R346T that does not mesh well with S:Q493E. I don't think it's a coincidence that S:H445R showed up simultaneously with R346T here. Historically, R346T has been nearly incompatible with N450D, for reasons that remain unclear. H445R is a significant shift toward more positive charge, so perhaps it somehow is able to neutralize whatever deleterious interaction R346T and N450D have.

Also worth noting is ORF1a:S1272G, a very rare mutation that when it appears, is often associated with chronic infections. Here it appears to have been acquired in circulation and is transmitting well.

Genomes - Note: There are still three sequences on Usher from New York that are not on GISAID. I'm pretty sure there's a lab in New York whose sequences never get uploaded to GISAID but which show up on Usher trees, so I'm not sure if these sequences will ever be on GISAID.

Genomes EPI_ISL_19217715, EPI_ISL_19217894, EPI_ISL_19221915, EPI_ISL_19231606, EPI_ISL_19262935, EPI_ISL_19273796, EPI_ISL_19277632, EPI_ISL_19284824-19284825
aviczhl2 commented 1 month ago

The parent is now KP.3.1.6

FedeGueli commented 1 month ago

13 on Gisaid that should mean 16. One sample from Switzerland via GBW

FedeGueli commented 1 month ago

14 on Gisaid with one more from Japan

New tree:

Screenshot 2024-07-30 alle 11 39 34

https://nextstrain.org/fetch/genome-test.gi.ucsc.edu/trash/ct/subtreeAuspice1_genome_test_cc37_8b2620.json?c=userOrOld&label=id:node_7023193

I count 21 of this manually on Usher.

FedeGueli commented 1 month ago

19 on Gisaid checking in USher this is quite fast. Here the new tree: https://nextstrain.org/fetch/genome-test.gi.ucsc.edu/trash/ct/subtreeAuspice1_genome_test_2d8ea_244150.json?c=userOrOld&label=id:node_7022137

Screenshot 2024-08-06 alle 17 48 23
Mydtlwn commented 1 month ago

At the same time, it has S:R346T and S:H445R, I think you'll be very interested. @corneliusroemer

FedeGueli commented 4 weeks ago

Designated MK.3 via https://github.com/cov-lineages/pango-designation/commit/2b11a9d8c2daa2f71ba63d0ddf96e61e4d43a0d0