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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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3 small clades with interesting (recombinant-look-alike) mutations #210

Closed c19850727 closed 3 years ago

c19850727 commented 3 years ago

Was browsing sequences in Korea and found something insteresting:

Proposed new lineage 1 Currently classified as B.1.619 Countries circulating: Korea (12 sequences) Earliest sequence: 2020/6/24 Most recent sequence: 2021/8/1 Mutations in addition to B.1.619: ORF8:V82A, ORF8:T120I, S:T19R Genomes: EPI_ISL_3026305, EPI_ISL_3026276, EPI_ISL_3026338, EPI_ISL_3545046, EPI_ISL_3026823, EPI_ISL_3026802, EPI_ISL_3026605, EPI_ISL_3026821, EPI_ISL_3026791, EPI_ISL_3026750, EPI_ISL_3544720, EPI_ISL_3545027 (2 of above 12 sequences have stretches of NNNs greater than 1%) image https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_1b19f_5504c0.json?c=gt-S_19&label=nuc%20mutations:C6628T,G10625A

Proposed new lineage 2 Potential sublineage of B.1.617.2 Countries circulating: Korea (9 sequences) Earliest sequence: 2020/6/29 Most recent sequence: 2021/8/2 Mutations in addition to B.1.617.2: S:I210T, S:T1027I, N:P13L, N:S201I, N:T205I Genomes: EPI_ISL_3026434, EPI_ISL_3026504, EPI_ISL_3026709, EPI_ISL_3026769, EPI_ISL_3026772, EPI_ISL_3026794, EPI_ISL_3026796, EPI_ISL_3026813, EPI_ISL_3545229 (1 of above 9 sequences has stretches of NNNs greater than 1%) image https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_3bb1_5694f0.json?c=gt-N_201&label=nuc%20mutations:C11514T BTW, there's another clade of Delta in Korea (around 50 sequences) that also has lost S:G142D/156del/157del/R158G, and instead gained I210T: image https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_6a2e_56ca60.json?c=gt-S_210

Proposed new lineage 3 Potential sublineage of B.1.617.2 Countries circulating: Spain (3 sequences), Belgium (1), Germany (1), France (1), Korea ex-UAE (1) Earliest sequence: 2020/6/10 Most recent sequence: 2021/7/29 Mutations in addition to B.1.617.2: ORF8:Q27stop, ORF8: R52I (6 out of 7 sequences), ORF8: Y73C (5 out of 7 sequences) Genomes: EPI_ISL_3388835, EPI_ISL_3646465, EPI_ISL_2885678, EPI_ISL_3646745, EPI_ISL_3451908, EPI_ISL_3634288, EPI_ISL_2635666 (EPI_ISL_3634288 and EPI_ISL_3646465 have long streches of NNNs) image https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_46868_2ac190.json?c=gt-nuc_27972 BTW, there are 3 other clades of Delta that have ORF8:Q27stop (maybe convergently?): https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_5692a_5738e0.json?c=gt-nuc_27972 (Denmark) https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_39633_2bb3f0.json?c=gt-nuc_27972 (the UK) https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_551a3_2ba470.json?c=gt-nuc_27972 (the US)

InfrPopGen commented 3 years ago

Thank you for the interesting comments and for highlighting these clusters. At present none of the three proposals meet the criteria for lineage designation. A summary of the reasons is given below.

Proposal 1: This proposed lineage branches from a B.1.619.1 basal lineage and is associated with S Korea; however, it also has affinities with the primarily AY.4 sub-tree nearby (which comes off a B.1.1.7 stem). Although it is a clade, exclusively Korean, and appears to have expanded recently relative to other clusters within its parent sub-tree, none of the defining mutations is a VOC or VOI, nor is there an association with an outbreak, phenotype or other epidemiological significance. The defining mutations are also found in a large adjacent sub-tree with global membership. Consequently, the proposal does not meet the epidemioliogical relevance criterion for designation. In addition, the genomes appear to lie in an improperly resolved region of the global tree and topological rearrangments are likely should additional samples become available (sister lineages include clusters of B.1.628, B.1.258.x, and local cluster also has B.1.525, B.1.415.1, B.1.1.291, B.1.177, A.1, A.2, A.2.2 and more!). This proposed lineage is worthy of occasional monitoring.

Proposal 2: This proposed lineage branches from an AY.4 basal lineage and is associated with S Korea. Although S:T1027I, on the branch leading to the proposed lineage does define a clade of entirely S Korean samples; this also defines two other clades within the parent sub-tree (and scattered across it), and these have international representation. The proposed lineage involves no current VOCs or VOIs, except for those typical of B.1.617.2. The suggestion is that the lineage proposed is in fact paraphyletic and the global phylogeny is not well resolved in this region. Consequently, designation as a lineage should be deferred until some epidemiological significance can be demonstrated and/or the surrounding phylogeny is clarified (e.g. by more samples).

Proposal 3: This proposed lineage lacks a definitive substitution (not likely a clade), has too few potential members and no epidemiological significance.