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Repository for suggesting new lineages that should be added to the current scheme
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Proposal for a AY.33 Sublineage with Spike H49Y and E654K (66 Seqs, ~17% Prevalence in Reunion) #370

Closed c19850727 closed 2 years ago

c19850727 commented 2 years ago

Description Sub-lineage of: AY.33 Earliest sequence: 2021/10/12 (France) Most recent sequence: 2021/11/29 (France-Reunion) Countries circulating: France (mainly in Reunion with ~17% prevalence, also in European France and Martinique)

Substitutions on top of AY.33:

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Gene | Mutations -- | -- ORF1a | S1306F, S3309P, M3616V ORF1b | V2515L, T284I, H1807R S | H49Y, E654K ORF7a | 54/76del nuc | C10525T, C17439T

(I am not sure if ORF7a:54/76del is real or artefactual though).

Genomes: EPI_ISL_5635915, EPI_ISL_5691147, EPI_ISL_5749178-5749179, EPI_ISL_6124361, EPI_ISL_6124452, EPI_ISL_6251031, EPI_ISL_6254128, EPI_ISL_6254232, EPI_ISL_6309697, EPI_ISL_6332445, EPI_ISL_6372467-6372468, EPI_ISL_6372476-6372478, EPI_ISL_6372480, EPI_ISL_6470406, EPI_ISL_6470408, EPI_ISL_6470784, EPI_ISL_6470867, EPI_ISL_6470886, EPI_ISL_6605077, EPI_ISL_6605136, EPI_ISL_6605173, EPI_ISL_6651171, EPI_ISL_6728028, EPI_ISL_6728040, EPI_ISL_6733147, EPI_ISL_6733152, EPI_ISL_6733162, EPI_ISL_6779419-6779421, EPI_ISL_6779423, EPI_ISL_6779444-6779445, EPI_ISL_6779816-6779820, EPI_ISL_6779843-6779844, EPI_ISL_6779877, EPI_ISL_6779897, EPI_ISL_7138675, EPI_ISL_7151165-7151166, EPI_ISL_7151171, EPI_ISL_7209359, EPI_ISL_7210207, EPI_ISL_7218491, EPI_ISL_7368649, EPI_ISL_7371249, EPI_ISL_7374143, EPI_ISL_7374532, EPI_ISL_7457319, EPI_ISL_7606746, EPI_ISL_7607624, EPI_ISL_7607712, EPI_ISL_7608045, EPI_ISL_7608711, EPI_ISL_7609233, EPI_ISL_7611266, EPI_ISL_7611272

Evidence Down-sampled tree as per Neherlab (France, filtered to AY.33): image Geographical prevalence as per Neherlab (in yellow coloer): image https://nextstrain.org/groups/neherlab/ncov/france?branchLabel=none&c=gt-S_49&f_pango_lineage=AY.33&label=Spike%20mutations:T29A,%20T250I&p=full&r=division&tl=division

Transmission advantage as per cov-spectrum: image

Usher tree: image https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_3fcd9_8cb870.json?c=gt-S_654&l=radial&label=nuc%20mutations:G210T,C241T,C3037T,G4181T,C6402T,C7124T,C8986T,G9053T,C10029T,A11201G,A11332G,C14408T,G15451A,C16466T,C19220T,C21618G,A21647G,C22311T,C22458T,T22917G,C22995A,G23401T,A23403G,C23604G,C25469T,T26767C,T27638C,C27752T,C27874T,A28461G,G28881T,G28916T,G29402T,G29742T

chrisruis commented 2 years ago

Thanks @c19850727 We've added this as AY.33.1 in v1.2.114 to start on the branch with T10190C (Orf1ab:S3309P), A11111G (Orf1ab:M3616V), C14318T (Orf1ab:T4685I), C17439T (synonymous) and C21707T (S:H49Y)