It comes amid a rise in hospitalisations and a warning from health chiefs that the pandemic is “not over”.
The Omicron sub-variant, officially called BA.2, accounted for 57% of cases in England in the last week of February, up from a quarter just two weeks before, according to research by the Wellcome Sanger Institute.
Stealth Omicron got its nickname because it is more difficult to differentiate from Delta than the original Omicron variant, BA.1.
It is also more contagious but early studies seem to show no greater risk of hospitalisation, according to the UK Health Security Agency (UKHSA).
Dr Jenny Harries, its chief executive, said cases had declined substantially from the peak of the Omicron wave.
She said: “However, the increasing presence of the BA.2 sub-lineage of Omicron and the recent slight increase in infections in those over 55 show that the pandemic is not over and that we can expect to see Covid circulating at high levels.”
Professor Paul Elliott, director of Imperial College London’s React programme, said England is also seeing a rise in hospitalisations and warned that the BA.2 variant needs to be tracked carefully.
He added: “It is more transmissible. We are seeing an uptick in infections, particularly in the older group, and we are seeing an uptick in hospitalisations.
“At the moment, we’re possibly seeing the beginning of an uptick, but we don’t know where it’s going to go.”
The Wellcome Sanger Institute analysed 27,000 positive Covid-19 tests taken in the week to February 26 to determine which variant they were.
Areas with fewer than 10 samples have been omitted.
Here are the 16 areas which had the highest percentage of the strain, according to the data.