There has been considerable interest in the new Omicron variant of coronavirus (COVID-19), and when the Office for National Statistics' Coronavirus Infection Survey will be able to provide estimates on its prevalence in the UK.
Exact identification of a COVID-19 variant requires genome sequencing, which takes longer than identifying the gene pattern detected in our tests. Each week, we identify patterns of three genes in positive COVID-19 test results. These genes are the S gene, the ORF1ab gene and the N gene.
Delta variant infections usually test positive for all three genes, whereas the new Omicron variant is known to test negative for the S gene. To date, around 99% of positive COVID-19 infections in the UK are the Delta variant. If our weekly monitoring of gene patterns shows a decreased detection of the S gene, this could be an indication of the Omicron variant.
Among milder infections of the Delta variant, there may not be enough virus collected on swabs to detect the presence of the S gene. Therefore, we advise caution against drawing conclusions from small changes in the absence of an S gene. This could be caused by Delta variant infections with a low viral load, or other less common variants in circulation such as the Alpha variant.
A high viral load combined with the absence of an S gene will provide the first indication that the Omicron variant is increasing in prevalence among the UK population. Full sequencing will then be required to confirm if these cases are the Omicron variant.
Read more about how we identify variants from the Coronavirus Infection Survey here.