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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 2 potential sublineages of B.1.1.7 circulating in France #183

Closed c19850727 closed 3 years ago

c19850727 commented 3 years ago

Proposed new sublineage 1 Currently classified as B.1.1.7 (63 sequences in France, 2 in Belgium and 1 in Spain) Earliest sequence: 2021/6/8 (France) Most recent sequence: 2021/7/24 (France) Mutations in addition to B.1.1.7: N: H300Y ORF8: V62L, 66/67DEL, K68E Some of the more recent sequences (since 2021-07-06) have the following additional mutations: N: A35V ORF1a: A2379V ORF1b: P1223L ORF9b: R32C, A57V No mutations on spikes though. Genomes: B.1.1.7 proposed sublineage 1.csv Evidence: image https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_577a8_7778f0.json?c=gt-N_35,300&tl=country

Proposed new sublineage 2 Currently classified as B.1.1.7 (14 sequences in France) Earliest sequence: 2021/4/15 (France) Most recent sequence: 2021/7/8 (France) Mutations in addition to B.1.1.7: ORF1a: E2268D ORF3a: W131L ORF7a: S81P ORF8: K68stop S: A163V, M177T, L303F, V308L, G485V Some of the more recent sequences (since 2021-6-18) also have the following additional spike mutations: S: P251L, Y449H, N460K Genomes: B.1.1.7 proposed sublineage 2.csv Evidence: image https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_686b6_68dd20.json?c=gt-S_163,177,303,308,449,460,485

shay671 commented 3 years ago

Regarding the second variant - I see that it has 3 mutations in the RBD.
In all variants seemed so far (variants from the first generation, not variant based variants) there was no more than 3.

I run a scan of the last B.1.1.7 sequences, And i have to say that it repeats in some variants there that was evolved from B.1.1.7. It seems that this virus has still a lot to evolve.

chrisruis commented 3 years ago

Thanks @c19850727. We've added your sublineage 1 as Q.6 and your sublineage 2 as Q.7 in v1.2.66.

In both cases, we've taken the ancestor of the lineage back to start with a clear introduction(s) into France. For Q.6, this coincides with C29171T (N:H300Y) and for Q.7, this coincides with A7069C (Orf1ab:E2268D). Therefore Q.7 is wider than your proposed sublineage 2 but as the proposed sublineage 2 only contains a small number of genomes over several months, we haven't given this a further designation at this stage.

Thanks again for submitting