Potential Delta (AY.4) and Omicron recombinant

Description

Sub-lineage of: AY.4
Earliest sequence: 2022-01-17 (France | EPI_ISL_9959921 | EPI_ISL_9879436)
Most recent sequence: 2022-02-05 (Netherlands | EPI_ISL_9863764)
Countries circulating: Denmark / France / Netherlands
Proposed Lineage: If this is real, XD or whatever is next on the PANGO recombinant designations.

I don't have access to the raw sequencing reads to these strains so unsure if this is a real recombinant. However, these strains are highly related and are present in 3 countries in Europe. Additionally, these strains were sequenced in different laboratories with different sequencing platforms (Illumina: EPI_ISL_9879436, EPI_ISL_9879437, EPI_ISL_9857381, EPI_ISL_9449070, EPI_ISL_9166910) and (Nanopore MinION: EPI_ISL_9863764, EPI_ISL_9791275).

NextClade identifies these strains as 21J (Delta) and Pangolin v3.1.20 in UShER mode classifies these as AY.4.

NextClade Alignment of these sequences with some complete/high coverage genomes of Delta and a BA.1 (PHEC-5P0B7ZEF) and BA.2 (ALDP-35D5DD2):

The breakpoint appears to be right before the S gene.

Zooming in on the S gene:

Genomes

accessions_list.txt

Additional Mutations

This small cluster shares this mutation in addition to characteristics of Omicron spike mutations.

Phylogenetic Tree

Potential recombinant lineage in the context of other strains (embedded within AY.4)

Zoomed in:

Greater tree (strains highlighted by red box):