Description
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
Additional Mutations
| Gene | AA Changes |
|---|---|
| NSP2 | E172D |
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):
