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

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Photograph: Dan Himbrechts/AAP© Provided by The Guardian Photograph: Dan Himbrechts/AAPSo do we know how many of Australia’s latest cases are due to Omicron, and if it’s the dominant strain in the country yet?

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

First, some background on how we detect Omicron and other variants. The Omicron variant shares a characteristic mutation with another, older variant of concern called Alpha. Both variants have a mutation in the “S gene”, which means they show up differently to other coronavirus variants when using one of the common PCR tests used to check for Covid-19.

This means that we can use the absence of the S gene, called “S gene dropout” or “S gene target failure” as a proxy for tracking the rise of the Omicron variant. Some countries, such as the UK, have used this information to estimate the prevalence of Omicron over time.

However, only full genome sequencing can conclusively identify the strain – this means the whole genome of the virus is identified, rather than the presence of small, specific parts of the genome used in PCR.

Australia doesn’t publish S gene dropout numbers, but most positive cases undergo sequencing. As at June 2021 at least 58% of cases had been sequenced. Some information on variants of concern is then published by the communicable diseases genomics network. As of their update on 20 December, 386 Omicron cases had been identified, most in NSW.

Unfortunately this data only includes totals for the whole pandemic, so it can’t be used to show the proportion of Delta or Omicron in recent cases.

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 most recent 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.

“For example, Victoria and NSW are both sub-sampling a portion of the positive cases due to the high case numbers.

“There may be some biases in the sampling particularly recently, as samples are screened with PCR tests, and possible Omicron samples (such as S-gene target failures or dropouts) are prioritised for sequencing, so current sequences may not reflect the true underlying population.”

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 most recent data shows Omicron accounted for 45 out of 58 cases that have been sequenced and published since 13 December, or 78%.

To put the total number of sequenced cases into perspective, and emphasising that the most recently published figures are only a small fraction of total cases, here is the same data but showing the total numbers, rather than percentages.

This data will change as more cases are added to the database, and it may be that Omicron cases will still be outnumbered by Delta for the next few weeks. However scientists expect Omicron to become the dominant strain in Australia.

Associate prof Stuart Turville, a virologist at the Kirby Institute, says: “Even among vaccinated populations it is likely that Omicron will take over as the dominant variant. We should expect to see significant community spread.

“Day by day we’ll know more, but for now, people should follow government advice on boosters, social distance, wear masks where appropriate and follow the public health orders.”

In NSW, health authorities have already said they believe Omicron “likely accounts for the majority” of recent cases.

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