Patchy testing sparks growing fears Omicron hotspots are going undetected in Aylesbury Vale

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.

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.

A total of 220,781 PCR specimens taken in Aylesbury Vale were sent to labs between 1 July to 28 November 2021. Of those 88,099 specimens were sent to labs which test for S-gene dropout - 39.9% higher than the national average.

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

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.

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 Omicron

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.

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

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.

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

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.”