Only half of UK testing facilities are able to carry out genetic sequencing of positive PCR tests, which is needed to identify the variant feared to be more transmissible and, to some extent, vaccine-evasive.
It means only 10-20 per cent of positive results are sequenced, although a further 10 per cent are assessed for the absence of the S gene, cases which are likely to be omicron.
The health secretary Sajid Javid acknowledged the gap in sequencing and told MPs he is “expanding” other omicron testing methods to all centres, but was unable to say when that will happen.
The admission came as Mr Javid said there were 336 confirmed omicron case across the UK – a number which is likely to be a severe underestimation.
“This includes cases with no links to international travel. So, we can conclude that there is now community transmission across multiple regions of England,” he told parliament.
Some would be “feeling ill” while others have no symptoms, he told MPs, adding: “None of them, as far as I am aware, have been hospitalised.”
The update came as No 10 confirmed that laws requiring mask-wearing and costly travel tests will remain in place into the new year without a Commons vote if necessary.
Ministers had vowed to lift the restrictions before Christmas if possible, but their own scientific advisers have warned it will take longer to assess the threat from the omicron variant.
Mr Javid said the picture is still uncertain, but “the window between infection and infectiousness may be shorter for the omicron variant than for the delta variant”.
“We don’t yet have a complete picture of whether omicron causes more severe disease or, indeed, how it interacts with the vaccines,” he said.
“We can’t say for certain at this point whether omicron has the potential to knock us off our road to recovery.
“We are leaving nothing to chance. Our strategy is to buy ourselves times and to strengthen our defences while our world-leading scientists assess this new variant and what it means for our fight against Covid-19.”
The UK Health Security Agency told The Independent that only 10-20 per cent of positive PCR tests undergo genomic analysis because labs lack the capability.
Meanwhile, the latest Covid figures revealed 51,459 new coronavirus cases, which means the trend over the past seven days is 9.1 per cent up on the previous seven days.
The 811 new hospital admissions and 41 deaths within 28 days of a confirmed lab result mean both are still on a downward trend – but only just.
The emergency regulations, announced on 27 November, mean confirmed and “suspected” contacts of omicron cases must isolate for 10 days. However, it can take more than one week to carry out genetic sequencing – and there are thought to be stark regional differences in how likely that is to take place.
In his Commons statement, Mr Javid said the government is using “other methods” to detect likely omicron cases, such as the presence or absence of the S gene.
“We are expanding that as well so that all testing centres will be able to do it very soon,” MPs were told.
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