Potential Delta/Omicron Recombinant Lineage with Likely Breakpoint at NSP3 (11 Seqeuences in the US as of 2022/03/08)

[c19850727]

Description
Recombinant between: AY.x (my guess is AY.44, based on Nuc mutation A4015G) & BA.1.1
Earliest sequence: 2021/12/24 (US-MA)
Most recent sequence: 2022/1/18 (US-UT)
Countries circulating: US, MA and UT (6 sequences)

Likely breakpoint: between 5585 and 6511 (NSP3), which is different from other potential Delta/Omicron recombinant lineages.

Conserved Nuc mutations and AA changes (those in red frames are likely from the donor from the Delta side):

Evidence
Usher tree:

Genomes: EPI_ISL_9239635, 9244653, 9519590, 9677708, 9677356, 9677623, 10378301, 10654168, 10779170
And there are 2 additional sequences (flagged by @FedeGueli, many thanks!) that lack nuc C100T and G210T but otherwise matches other parts of the mutation profile: EPI_ISL_9150488, 9678032.

[corneliusroemer]

Quick covSpectrum query for monitoring (doesn't catch all, only gives 4 sequences instead of 6 or 8, but better than nothing): https://cov-spectrum.org/explore/World/AllSamples/Past6M/variants?nucMutations=3505T%2C4015G%2C28732T

Here are corresponding Genbank sequences in Nextclade:
https://clades.nextstrain.org/?dataset-name=sars-cov-2&input-fasta=https://lapis.cov-spectrum.org/open/v1/sample/fasta?genbankAccession=OM647790,OM647768,OM647353,OM647096

[c19850727]

11 sequences now, and submitted from MA, UT, CA and HI.

[AngieHinrichs]

@ktmeaton pointed out in lenaschimmel/sc2rf#8 that most sequences in this cluster have not only 5584G associated with Nextstrain clade 21I, but also 4181T associated with 21J, and that makes for a confusing picture in the awesome sarscov2recombinants tool. But thanks to covSPECTRUM I think I have found a plausible Delta parent clade in 21J that acquired 5584G (I'm guessing as a recurrent mutation but then I haven't tried to find a recombination event that would explain it...).

Here is a covSPECTRUM query that finds (mostly AY.44) sequences with 4181T and 5584G as well as mutations 3505T and 4015G that are shared by these sequences:

https://cov-spectrum.org/explore/World/AllSamples/Past6M/variants?variantQuery=3505T+%26+4015G+%26+5584G+%26+4181T

Here's an UShER/Nextstrain view of the branch in AY.44 that has those 4 mutations:
https://nextstrain.org/fetch/hgwdev.gi.ucsc.edu/~angie/pango-designation-446_possibleDeltaParent.json?c=pango_lineage&label=nuc%20mutations:A4015G

And here's a view of the branch with the proposed recombinant from this issue, down near the bottom, blue with one red uploaded sample (I suggest zooming in one more level to the node with G210T and turning on nucleotide mutation branch labels; direct link doesn't work because the tree has more than one G210T node):
https://nextstrain.org/fetch/hgwdev.gi.ucsc.edu/~angie/pango-designation-446.json?c=pango_lineage_usher&label=nuc%20mutations:G4181T

[chrisruis]

Thanks @c19850727 It looks like there's still only 12 genomes in this recombinant so will close this for now