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expert reaction to UKHSA update on Omicron risk assessment and S-gene target failure

The UK Health Security Agency (UKHSA) has published an updated risk assessment for the Omicron variant and S-gene target failure.


Dr Simon Clarke, Associate Professor in Cellular Microbiology, University of Reading, said:

“This UKHSA technical report highlights how some PCR testing used to diagnose Covid-19 can be used to detect the Omicron variant.  A phenomenon of S-gene target failure (SGTF) happens when PCR is carried out on Omicron because its S-gene has a small deletion in it which means the reaction doesn’t work with this particular gene.  However this test is only used in 4 labs, so there are geographical dead spots where it’s not possible to use SGTF to monitor the Omicron situation.

“UKHSA report that SGTF can be used successfully to monitor spread of the Omicron variant at a time when rapidly monitoring its spread is of such importance.  The fact that the number of cases detected by this method increased nearly 5-fold in a matter of a couple of weeks shows how it can give timely data on the spread of this new variant.  Data like that is extremely useful in determining transmissibility and the scale of any growth advantage and has been used to update their risk assessment to suggest that Omicron has a significant growth advantage over the delta variant, which could allow it to outcompete delta.  This has clear consequences for public policy and management of the pandemic.

“When it became apparent that Omicron could be distinguished from other variants using SGTF, the fact that coverage is not ubiquitous across the country was cited as an excuse as to why such a strategy wouldn’t work.  Here the UKHSA show how it can be used successfully to tackle the new variant.  Given the concern surrounding Omicron, it would be a very good idea to test for SGTF in more laboratories.”


Dr Julian Tang, Honorary Associate Professor/Clinical Virologist, Respiratory Sciences, University of Leicester, said:

“The ‘S gene target failure’ (SGTF) or ‘S gene drop out’ is seen in labs using the TaqPath assay to detect SARS-COV-2 variants that contain the S gene 69-70del mutation:

“This assay uses two other SARS-COV-2 gene targets (N and ORF1ab) that can detect the virus – so the diagnosis is not actually missed.

“The alpha variant was the other common variant in the UK that had this same 69-70del mutation and some of it might still be around – but these are very few:

“So where the alpha variant is now mostly absent, this SGTF testing profile can be used to detect omicron.

“However although the TaqPath assay is used in most community light house testing labs, hospital labs may use a different assay that does not target the S gene – so this SGTF profile will not be available for some hospitalised cases.

“So estimates of National UK omicron case numbers, just based on this SGTF profile testing, will likely underestimate the total number of omicron cases in the UK.”



All our previous output on this subject can be seen at this weblink:



Declared interests

None received.

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