Fears over undetected Omicron hotspots in southern England as patchy testing regime revealed

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Only a fraction of PCR swabs from some parts of England are tested for a key sign of the ‘highly infectious’ variant, leading scientists to fear that geographical outbreaks are going under the radar.

Some parts of England are only sending one in 100 Covid tests to labs that can identify potential Omicron cases.

It has raised fears among scientists that hotspots of the “highly infectious” variant could be going undetected, particularly in the South West and South East.

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About one in every six positive PCR tests are sent for genome sequencing to determine which variant they are - a process which can take many days.

A quicker way to spot potential Omicron cases is to look for a marker called the S-gene, which is missing in variants such as Omicron and Alpha but present in Delta cases.

Once identified, swabs showing so-called ‘S-gene dropout’ can then be sent for definitive testing for Omicron.

Four UK labs use a Covid testing system which detects the S-gene - at Newcastle, Milton Keynes, Glasgow and Alderley Park in Cheshire.

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But only about a third of PCR swabs are sent to one of these sites, rather than other labs, with the proportion varying widely across the country.


Use of these labs is particularly low in the South West and parts of the South East, raising fears that Omicron hotspots could be going undetected.

According to the UK Health Security Agency, just 1% of PCR tests from Cornwall were sent to these four labs from July 1 to November 28.

This compares to 72% in Hartlepool.

Prof Rowland Kao, of the University of Edinburgh, who contributes to the Scientific Pandemic Influenza Group on Modelling (Spi-M) government advisory group, told The Guardian that geographical patchiness of S-gene dropout testing was a concern.

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He said that “if we want to slow down the spread of Omicron in the UK, we need to be able to identify geographical clusters”.

Health Secretary Sajid Javid told the Commons on Monday that labs had now brought in other methods to try to detect the new variant.

He said this capability was being expanded so that all testing centres would be able to pick it up “very soon”.

The Covid-19 testing lab at Queen Elizabeth University Hospital in Glasgow is one of only four in the UK testing for the S-gene, a marker of OmicronThe Covid-19 testing lab at Queen Elizabeth University Hospital in Glasgow is one of only four in the UK testing for the S-gene, a marker of Omicron
The Covid-19 testing lab at Queen Elizabeth University Hospital in Glasgow is one of only four in the UK testing for the S-gene, a marker of Omicron | Getty Images

The HSA said that in the week to December 6, 705 swabs had been found to have S-gene dropout, most in London and the South East.

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But it acknowledged that attempts to identify trends are “affected by the coverage of laboratories contributing to this surveillance data”.

A spokesperson said: “All samples from international arrivals to the UK, contacts of suspected and confirmed cases will have their samples analysed by labs that can detect suspected Omicron cases.

“These samples will be sent for sequencing to confirm the initial results.

“We are constantly reviewing our laboratory testing capacity and capability to ensure that the COVID-19 testing programme is as effective as possible.”

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Omicron is likely to replace Delta as the dominant strain and is set to be responsible for at least half of UK coronavirus cases in the next two to four weeks, according to the UK Health Security Agency (HSA).


Javid warned yesterday that Omicron cases within the UK could “exceed one million” by the end of December.

Immune protection - either through vaccination or having had the virus before - is also lower with Omicron than with other variants, early research shows.

It is not yet known whether Omicron brings a greater or lesser risk of serious illness or death.

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The HSA’s 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.”

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