Delta variant AY.36 sub-lineage proposal mainly circulating in Germany

[genomesurveillance]

It is necessary to designate this AY.36 sub-lineage as this sub-lineage occurred in Germany, increased quickly in Germany, and then spread to the rest of Europe, which is different from original AY.36 (dominant in Nigeria and spread to UK and a few countries in the rest of Europe),

Description
Sub-lineage of AY.36.
Earliest sequence: Germany 2021-10-04.
Most recent sequence: Current
Countries circulating: mainly in Germany, also in multiple other European countries.

In addition to AA substitutions shared with AY.36: S: 1104L, orf1b:721R, orf1b:1538L
This sub-lineage has four additional AA substitutions: orf9b: 3S, orf3a: 223I, orf1a: 944L, N: 6L.

country_frequency_AY36withN_P6Lupdate.xlsx

Genomes(~1885)
AY36sublineage_withN_P6L.ods

Evidence
Comparing this new AY.36 sublineage (on the top right) with AY.36, AY.20 and AY.4. Phylogney was built with earliest samples belonging to these lineages.

1. Colored by country.
   

2. Displaying mutation N_P6L.
   

3. Displaying mutation ORF1a_S944L.
   

Suggested name of this AY.36 sub-lineage:AY.36.1

[genomesurveillance]

County frequency of this AY.36 sub-lineage (based on information till 2022-02-08):

Country	Total Variant Sequences	First seq. found at	Last seq. found at
Germany	1486	2021-10-04	2022-01-20
Denmark	271	2021-10-25	2022-01-05
United Kingdom	30	2021-10-04	2021-12-18
Czech Republic	28	2021-10-23	2022-01-24
Switzerland	14	2021-11-06	2021-12-04
Croatia	13	2021-12-09	2021-12-29
Poland	12	2021-11-24	2022-01-19
Italy	5	2021-11-11	2021-12-20
France	4	2021-11-22	2021-12-27
Netherlands	4	2021-11-10	2021-12-16
Lithuania	2	2021-12-07	2021-12-22
Slovenia	3	2022-01-03	2022-01-10
Spain	2	2021-11-26	2021-12-14
Austria	1	2021-12-16	2021-12-16
Romania	1	2021-12-14	2021-12-14

[FedeGueli]

Hi thanks for highlighting and adding your precious analysis.
I have already proposed this sublineage in #407 and i agree very much that this is worth a designation.
Me and @bitbyte2015 checked with cov-spectrum all the designated and proposed sublineages of Delta vs Delta baseline and this one resulted to be one of the more trasmissible ( there is a potential bias toward apparent trasmissibility in these last lineages on covspectrum cause the former high trasmissible lineages have been hit hard and before the others in Uk and Dk by Omicron and Ba.2, and the share of sequences of Dk and Uk is the most important on the global number of sequences).
@chrisruis

[genomesurveillance]

Will be great this AY.36 sub-lineage got its own name.....it is still circulating in Germany.

[FedeGueli]

@corneliusroemer @chrisruis Probably this deserves a designation: proposed here and in #407 .
Recently AY.36 has been described in a paper published on Nature regarding Nigerian uncommon lineages.
A designation of this clade could help authors if they will update their analyses in future.

[corneliusroemer]

I agree, this could be designated, though with only 1.8k sequences it's not that big a lineage, so I'm on the fence.

AY.36* seems to have been as competitive as AY.4.2* in Germany which is interesting.

@chrisruis what do you think?

https://cov-spectrum.org/explore/Germany/AllSamples/Past6M/variants?pangoLineage=B.1.617.2*&aaMutations1=Orf3a%3AT223I%2CN%3A6L&pangoLineage1=AY.36*&pangoLineage2=AY.36*&pangoLineage3=AY.4.2*&analysisMode=CompareToBaseline

[FedeGueli]

@corneliusroemer 3 last seqs are from 2 countries (Ger, Cz) in february22

EPI_ISL_9963879
EPI_ISL_10007727
EPI_ISL_10012839

[FedeGueli]

Interestingly the last two seqs from germany do not cluster together confronting this tree to this one
The czech sequence clusters indepently from both german samples

[genomesurveillance]

The variant had grown very rapidly in our local samples till recently when Omicron became dominant. Indeed, it is as competitive as AY.4.2*, and the local spreading pattern is also quite special.

[chrisruis]

Thanks @genomesurveillance I agree this warrants a designation. We've added this as AY.36.1 in v1.2.131 to start on the branch with C28290T (N:P6L)

[genomesurveillance]

I could not detect AY.36.1 with the newest release v1.2.131, also I did not find AY.36.1 in the lineages.csv file. Can you please have a check @chrisruis ?

[chrisruis]

Hi @genomesurveillance Just had a look and AY.36.1 is in the lineages.csv for v1.2.131. Sequences won't be assigned to AY.36.1 with pangolin until there's a new run of pangoLEARN which we run every week or two. So sequences won't be assigned to AY.36.1 yet. It should appear in pangolin when the pangoLEARN release (which you can see here) includes v1.2.131

[genomesurveillance]

@chrisruis Thank you very much for the quick feedback!