Australia: possible Queensland Deltacron cluster identified *1 UPDATE*

Australasia, Australia, BA.1, BA.2, Coronavirus, Delta, Deltacron, Genome, Infection, Omicron, Queensland, Recombination, Transmission

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.

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

** This post was originally published on February 14, 2022 **