Proposal for a potential sublineage of AY.34 with S:T859I (~500 sequences, ~42% prevalence in Martinique)

[c19850727]

Description Sub-lineage of: AY.34 (489 sequences) Earliest sequence: 2021/4/19 (the UK) Most recent sequence: 2021/9/28 (Martinique) Countries circulating: mainly Martinique (217 sequences) and France (102 sequences)

Cumulative prevalence and number of samples sequenced as per Outbreak.info:

Mutations in addition to Ay.34: nuc G19563A, then ORF1b:T2548I, then ORF1a:V3718F and S:T859I

Genomes: AY.34+T859I.csv

Evidence Downsized tree as per NeherLab: https://nextstrain.org/groups/neherlab/ncov/france?c=gt-S_859&p=grid&r=division

UShER sub-tree: https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_3bd0a_ef8c10.json?c=gt-S_859&l=radial

[corneliusroemer]

Can you zoom your screenshots in and enable AA muts on the branches, right now the screenshots aren't as useful as they could be. There's a sister lineage that may also be worth designating, with nuc:19602T and common in Europe/France https://nextstrain.org/groups/neherlab/ncov/france?branchLabel=aa&c=gt-nuc_14457,11417,19602&label=spike_mutations:Q677H&m=div&r=division

Generally, there's quite a bit of interesting diversity within AY.34 which lends itself to a few sublineages. This lineage seems to have acquired quite some diversity in Africa.

https://nextstrain.org/groups/neherlab/ncov/africa?branchLabel=aa&c=gt-nuc_15908,21987,16512,14457&m=div&tl=pango_lineage

These are the nuc mut sites that separate the branches, could lend themselves for defining AY.34.1/2/3/4 etc: 15908, 21987, 16512, 14457

[chrisruis]

Thanks @c19850727 We've added this as AY.34.2 in v1.2.103 to start on a branch with G11417T (Orf1ab:V3718F) which coincides with the clade containing the Martinique sequences

[FedeGueli]

@chrisruis @corneliusroemer

Put this here, cause i am not sure if i'll go proposing it, but it is surely worth a mention In november a sublineage of AY.4 with the same mutation S:T859I was on the raise in Denmark reaching around 4% in mid november. Covspectrum past 3m Interestingly the danish clade carried S:I101T too

To note that B.1.640 carries a different mutation in the same residue S:T859N