UK Health Security Agency News and Media

08 Dec 2021

UKHSA publishes update on Omicron risk assessment and S-gene target failure

UKHSA has published an updated risk assessment for the Omicron variant. The assessment suggests that Omicron is displaying a significant growth advantage over Delta, meaning that it is likely to outcompete Delta in the UK and become the dominant variant.

This assessment is based on analysis of UK data showing increased household transmission risk, increased secondary attack rates (i.e. the chance of each case infecting another individual) and increased growth rates compared to Delta. If the growth rate and doubling time continue at the rate we have seen in the last 2 weeks, we expect to see at least 50% of COVID-19 cases to be caused by the Omicron variant in the next 2-4 weeks.

The risk assessment also suggests that Omicron displays a reduction in protection offered by having had a previous infection or vaccination. Whilst there are insufficient data to quantify either vaccine effectiveness or risk of reinfection in the UK exactly, the observed growth, case distribution and early analyses in both South Africa and the UK are consistent with some loss of immune protection against infection. New studies are being undertaken to assess this further.

There are insufficient data to make any assessment of protection against severe disease, or to assess the severity of illness caused by Omicron. Further studies are underway in the UK and abroad.

In addition, UKHSA has published data which shows the detection of cases exhibiting S-gene target failure (SGTF) in recent weeks across the country. Approximately half of PCR tests in the UK are able to detect SGTF.

SGTF is a useful indicator of the presence of Omicron, because as a rule Delta cases have the S-gene and Omicron cases do not. However, it is not confirmatory as there are a number of other reasons that a sample might exhibit SGTF. For example, there are still a small number of cases of other variants, such as Alpha, in the UK which would also result in S-gene dropout or there is a lower amount of virus present in the sample where S-gene dropout cannot be confirmed.

Positive tests with sufficient virus detected from people arriving in the UK are sent for confirmation through Whole Genome Sequencing, regardless of the presence or absence of SGTF.

As part of UKHSA’s routine genomic surveillance, approximately 15-20% of all positive PCR tests are also sent for sequencing.

Until the week beginning 23 November 2021, the weekly count of cases with SGTF was routinely less than 150, making up less than 0.1% of all cases. Analyses of sequenced SGTF samples has indicated that until mid-November, more than 99% of these were Delta cases. 

In the most recent week of data (specimen dates from 30 November 2021 reported as of 6 December), the number of cases with SGTF has increased to 705. The majority of these cases are located in London and the South East.

Trends in SGTF over and time are however affected by the coverage of laboratories contributing to this surveillance data.

UKHSA Chief Medical Advisor, Dr Susan Hopkins said:

“It is increasingly evident that Omicron is highly infectious and there is emerging laboratory and early clinical evidence to suggest that both vaccine-acquired and naturally acquired immunity against infection is reduced for this variant. It is therefore absolutely critical that we all do everything that we can to help break the chains of transmission and slow the spread of this new variant.

“Vaccination is critical to help us bolster our defences against becoming severely ill from this new variant – please get your first, second, third or booster jab without delay. Please also make sure to follow all Government guidance to reduce the spread of infection.

“It remains vital that anyone with COVID-19 symptoms isolates and gets a PCR test immediately.”

Contact Information

Luke Weeks
Public Health England

Notes to editors

  • Since the emergence of SARS-CoV-2 virus and its global spread, the UK has shared more than 1.4M genomes with the public health and scientific community globally through GISAID, NCBI and ENA. We have been gradually increasing our sequencing capacity since March 2021 with the weekly upload of sequences increasing from 20K genomes per week to 64K last week and it will be closer to 80K by January 2022.   
  • In the UK, in total, we have sequenced 13.7% of all COVID-19 cases.  The percentage of the total PCR cases detected that has been sequenced each week has varied with incidence and follows a robust surveillance framework to detect cases on importation, random surveillance in the community, and surveillance of hospital laboratory testing.
  • Only 6 nations have sequenced over 100K genomes with UK contributing almost a quarter of the total GISAID genome content of 5.8M and globally, only the US has sequenced more than the UK.