We’ve seen several sequences collected early this year in Queensland, Australia being called Omicron unassigned by Pangolin and show similar patterns: ORF1ab mutations are more like from Delta with high alternate freq. However they’re far away from the aforementioned UK sequences (>20 SNPs):

Australia/QLD5084/2022 (Illumina)
Australia/QLD39476/2022 (ONT low qual.)
Australia/QLD37984/2022 (Illumina)
Australia/QLD0x00C42F/2022 (Illumina)

Not all of them are available on GISAID so here is the FASTA and VCF

A rough analysis based on scorpio haplotype of above 4 UK sequences and these 4 QLD sequences using AY.4 and BA.1 constellations:

suggesting that there are 2 different breakpoints from 2 independent recombinant events for UK and QLD sequences.

The low number of sequences may not strong enough for new lineage atm but will keep update if situation changes.

Github.com

Apart from the UK another "Deltacron" Delta / Omicron recombination variant has been found in Australia.

Just like the one monitored by UKHSA this one also show recombination in the Orf1ab polyprotein but also an additional Spike mutation: I1081Vhttps://t.co/zcnhHpUtQ5 pic.twitter.com/9JZbCaQ7Br

— Gönndalf 🇺🇦 (@drallcome) February 14, 2022

UPDATE 1 – 16th February 2022

There is an ongoing conversation on Github about the possible Australian recombinant sequences, which we have linked to below..

Github thread: Small Australian cluster (7 seq) of potential Delta-Omicron recombinants

Image by DroneImagineNation from Pixabay