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cov-lineages / pango-designation

Repository for suggesting new lineages that should be added to the current scheme
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Proposal for a Delta (21J) Sublineage with ORF7b E39stop and H42Q (~360 Seqs, ~1% Prevalence in Denmark) #379

Closed c19850727 closed 2 years ago

c19850727 commented 2 years ago

Description Sub-lineage of: B.1.617.2 (21J) Earliest sequence: 2021/10/25 (Denmark) Most recent sequence: 2021/12/11 (Denmark) Countries circulating: Denmark predominantly, and 2 sequences from Sweden

Substitutions on top of B.1.617.2:

Gene | Mutations -- | -- ORF1a | A385T, K636R, P1497S ORF1b | M1582I, I2147M ORF3a | D155Y ORF7b | E39stop, H42Q nuc | A2172G, C4754T, C7945T, G11161A, T11488C, T19500C, C23683T, C25710T

Evidence Usher tree: image

Uher tree displaying geographical distribution: image https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_2c6e6_3d7550.json?c=gt-ORF7b_42&l=radial

Down-sampled tree as per Neherlab doesn't work very well, as there are only 2 isolates of this potential sublineage included by its down-sampling. I have to use a scatter tree (filtered to B.1.617.2) to have a proper view of it: image

Mutation of the branch as per Neherlab: image https://nextstrain.org/groups/neherlab/ncov/denmark?branchLabel=none&c=gt-nuc_1418,27131&f_country=Denmark&f_pango_usher=B.1.617.2&l=scatter&p=full&r=division&scatterY=gt

Transmission advantage as per Cov-spectrum: image https://cov-spectrum-develop-git-lapis-and-refactoring-cov-spectrum.vercel.app/explore/World/AllSamples/AllTimes/variants?aaMutations=ORF7b%3AE39*%2CORF7b%3A42Q%2CORF3a%3AD155Y

InfrPopGen commented 2 years ago

Thanks for submitting. We've added lineage AY.132 with 305 newly designated sequences, in v1.2.119