London and the East Midlands are seeing the highest number of Omicron cases in England, official figures have revealed.
But some cases in the south west of England are being missed because the labs that detect the new strain have lower coverage for this region, the UK Health Security Agency said.
The largest Omicron cluster in England is in West Northamptonshire in the East Midlands, where there were 83 confirmed or suspected cases between 22 November and 5 December.
In eight boroughs in London, there have been 131 confirmed or suspected cases of the variant, with the largest clusters in Lewisham, with 26 cases and Newham with 22.
There have been 16 confirmed or suspect cases during this period in Greenwich, 16 in Lambeth, 14 each in Hackney and Brent, 13 in Wandsworth and 10 in Croydon.
A further 22 have been confirmed or suspected in Buckinghamshire in the south east.
Public health officials have been carrying out PCR testing of all close contacts of confirmed Omicron cases, and all have to self-isolate for 10 days.
Scientists are able to pick up suspected Omicron cases using a lab test called S-gene target failure (SGTF), which refers to the deletion of a gene that is normally picked up in a number of other covid variants including Delta.
The S-gene “dropout” has become a marker for identifying where Omicron is rising in an area compared to Delta.
While the proportions of SGTF samples remain below 5 per cent of all sequenced covid cases, the numbers are starting to increase as Omicron begins to spread within the community in the UK.
In the week ending 30 November, the number of SGTF samples leapt in several regions compared to the week before.
The Omicron variant was first identified in cases in Botswana and South Africa in mid-November, and although the UK placed southern African countries under flight bans on 25 November, the strain had already begun to be seeded in areas in the UK.
Until the week beginning 23 November, the weekly count of cases with S-gene target failure in England was less than 150 – likely to relate to the Alpha variant, which also has a similar gene deletion. A week later, this figure had risen to 705 due to the arrival of Omicron in the UK.
In London, there were 205 S-gene dropout cases, indicating possible Omicron cases, in the week ending 30 November.
The East Midlands, north west, south east and east of England all had around 100 SGTF cases each, while in the south west it was around 40, 27 in the West Midlands and less than 25 in Yorkshire and the Humber, while there was a handful in the north east.
The UKHSA said the real number of cases for the south west of England could be higher but the lack of coverage from labs was not picking up as many as in other regions.
In its latest technical briefing it says: “Trends in SGTF over space and time are however affected by the coverage of laboratories contributing to this surveillance data.
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“Currently, SGTF monitoring is based on data submitted by 4 laboratories: Alderley Park, Glasgow, Milton Keynes, and Newcastle Lighthouse Laboratories.
“Coverage of these laboratories is particularly low in the South West, which is a partial explanation for the low numbers of cases with SGTF seen in this region.”
A source said this was unrelated to the issue of the Immensa Lab in Wolverhampton, which analysed PCR test samples from the south west region and whose testing was suspended by the government in October due to a large proportion of false negatives. Immensa did not carry out SGTF tests.
But some cases in the south west would be missed because the Lighthouse Labs have lower coverage in this region, a source admitted.
However all positive tests from contacts of Omicron cases or from recent arrivals to the UK were being sent to labs capable of detecting SGTF, the source said.