New AY.X lineage with mutations ORF3a:G49V, ORF3a:T221K, S:T95I growing in India, Germany, Denmark, UK, US

[bitbyte2015]

Sub-lineage of: B.1.617.2
Earliest sequence: 2021-16
Latest sequence: 2021-45
Total sequences: 4706

A large proportion of AY.102 sequences with the above mutations are misclassified and the lineage appears to be growing across many European countries. The lineage appears to have emerged from India around April 2021 and was first detected in Germany in July 2021. Since then it has grown to 9% in India, 2% in Denmark, and 1% in Germany. It also appears to be recently emerging in the UK and US.

USHER puts it on an entirely new branch of B.1.617.2 but I'm not sure if S:T95I emerged independently or if it's a part of the existing S:T95I branch.

https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/singleSubtreeAuspice_genome_2cf05_c87280.json?branchLabel=Spike%20mutations

Transmission advantage is hard to determine but it appears to be around 10-15% for Germany.

https://cov-spectrum.ethz.ch/explore/World/AllSamples/Y2021/variants?aaMutations=ORF3a%3AG49V%2CORF3a%3AT221K%2CS%3AT95I

Gene	Mutation
ORF3a	G49V, T221K
S	T95I

Country	Sequences
India	552
Denmark	920
Germany	523
United Kingdom	745
United States	420

sequences(2).csv

Proposed Lineage Name: AY.X

[FedeGueli]

Nice catch.
ir seems growing in Switzerland

Denmark

Uk (although low numbers)

Considering the efficacy of sequencing in these countries and considering that especially in Uk the most trasmissible AY.s are widely circulating i think it deserves a designation @corneliusroemer

The branch of this lineage that seems growing faster carries also orf9b:R32L , unsure if it is better to include or exclude it from defining mutations

[FedeGueli]

Hi @corneliusroemer @chrisruis looking at the trend of this lineage in Denmark i think the designation is well supported:
(Denmark last month)

CovSpectrum

[chrisruis]

Thanks @bitbyte2015 We've added this as AY.127 in v1.2.105 to start on the branch with G25538T (Orf3a:G49V)