How much of the Omicron variant is there in Australia, and is it dominant?

The Omicron variant of Covid-19 is now the dominant variant in England, South Africa, and probably in the US, according to estimates from the Centers for Disease Control.

The short answer is that it may be but this comes with a lot of caveats.

Most of the Australian sequence data is shared internationally with a group called GISAID, a collaboration of scientists from around the world pooling Covid-19 genomic information to aid research and health responses. Thanks to another group of scientists who run the NextStrain and CoVariants websites that analyse the GISAID data, we can see the change in the proportion of variants of concern over time.

Before we take a look at the numbers, there are some important caveats. This sequencing data represents a sample of the overall Covid-19 case population, and there is a lag between when a case is identified and when the sequence data is published. This means the latest time points are incomplete.

Dr Norelle Sherry is a scientist at the Doherty Institute and physician at the Austin hospital who is involved with genomic sequencing for pathogen surveillance. She says there is also some variation in sequencing strategies between jurisdictions.

On 19 December NSW Health announced it would be undertaking genomic sequencing for the Omicron variant only in circumstances where it would make a clinical difference to the care of a patient.

With all that in mind, the latest data shows Omicron accounted for 45 out of 58 cases that have been sequenced and published since 13 December, or 78%.