Potential Sublineage of Issue #342 with Spike T859N (~550 seqs, 100% Prevalence in Djibouti)

[c19850727]

The parent lineage of this potential sublineage has been submitted by @bitbyte2015 in #342 , and is yet to be designated.

Description
Sub-lineage of: #342 (~550 sequences)
Earliest sequence: 2021/8/12 (Belgium)
Most recent sequence: 2021/11/19 (Norway)
Countries circulating: Djibouti (100% prevalence, based on very limited sequences), Sweden (~3% prevalence), Norway (~1.6% prevalence), and a few other European countries

Mutations in addition to #342 :

Gene	Substitutions
Spike	T859N
nuc	G242A, T7816C

Genomes:
#342+T859N.csv

Evidence

Transmission advantage as per cov-spectrum:

International comparison as per cov-spectrum:

https://cov-spectrum-develop-git-lapis-and-refactoring-cov-spectrum.vercel.app/explore/World/AllSamples/AllTimes/variants?aaMutations=S%3AT859N&nucMutations=G242A

Usher tree:

https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_2f990_5a05c0.json?c=gt-nuc_242&l=radial

[chrisruis]

Thanks @c19850727 The Djibouti sequences are in a subclade of the clade with S:T859N. It looks like the proportion of AY.127 sequences with S:T859N has stayed relatively constant so we haven't designated the complete AY.127 clade. We've instead started this lineage on the branch with A19445G (Orf1ab:K6394R) which likely coincides with the introduction(s) into Djibouti. We've added this as AY.127.1 in v1.2.114

[FedeGueli]

Hi @chrisruis cc @corneliusroemer @AngieHinrichs

I think things had changed since:
AY.127+S:T859N accounts now for 30% of total AY.127* sequences

i am going to open an issue to broaden AY.127.1 starting from S:T859 and to rename the branch of it with orf1b:k1993R AY.121.1.1