New Danish AY.X lineage that appeared to exhibit rapid growth before Omicron displacement (758 seq, 2% in Denmark)

[bitbyte2015]

Though out competed now, this Delta sub-lineage arose out of Denmark around the first week of November. It contains a long branch leading away from B.1.617.2 and only began to diversify after the acquisition of a second N gene mutation. In some regions of Denmark, it grew from first detection to 4% proportion in three weeks.

This lineage has a total of seven amino acid mutations with one reversion on a branch leading away from Delta consensus. They are listed below in the order they appeared:

Gene	AA Mutation
N	S183T
ORF1b	T2432I
ORF1a	S3173N
ORF7a	A82V
ORF7a	R80I
nuc	G4300T
nuc	C5869T
ORF1ab	K2059N
nuc	G14400T
N	T362I

*Italicized mutations were grouped together on the same branch by USHER

https://genome.ucsc.edu/cgi-bin/hgPhyloPlace?db=wuhCor1&phyloPlaceTree=hgPhyloPlaceData/wuhCor1/public.plusGisaid.latest.masked.pb&subtreeSize=1000&remoteFile=https%3A%2F%2Flapis.cov-spectrum.org%2Fgisaid%2Fv1%2Fsample%2Fgisaid-epi-isl%3Fhost%3DHuman%26orderBy%3Drandom%26limit%3D1000%26dateFrom%3D2021-10-11%26aaMutations%3DN%253AT362I%26nucMutations%3DG14400T%26pangoLineage%3DAY.*

Using the last two mutations on the branch, Covspectrum shows that only two countries have detected it - Denmark and Sweden with all but 8 in Denmark.

The proportion appears to have peaked around the start of December

https://cov-spectrum.org/explore/Denmark/AllSamples/Past3M/variants?aaMutations=N%3AT362I&nucMutations=G14400T

Nextclade also gives almost all sequences good QC status

Proposed Lineage Name: AY.X

[bitbyte2015]

contributors(1).csv
Here is a table of sequences

[FedeGueli]

This clade displays a good Growth rate advantage on AY.4.2* all sublineages baseline in Europe:

[InfrPopGen]

Thanks for submitting. We've added lineage AY.39.4 with 801 newly designated sequences. Defining mutation(s) N:T362I, ORF1ab:K2059N, ORF7a:R80I.

[InfrPopGen]

Reassigned to new lineage AY.134