Separate research in Scotland has found even higher rates, with nine in 10 cases now thought to be the more contagious strain - potentially explaining its recent record infection rates.
Figures from Public Health Scotland show that as of March 18, 90.1% of cases in Scotland exhibited a tell-tale sign of BA.2.
The analysis comes as coronavirus infections and hospitalisations surge across the UK, with researchers saying the contagious subvariant is a key reason for the spike.
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 for an infected person, according to the UK Health Security Agency (UKHSA).
Which regions of England have the greatest number of Stealth Omicron cases?
The Wellcome Sanger Institute analysed more than 41,000 Covid tests from the week ending March 12, taken from every part of England.
Regionally, London had the greatest proportion of samples testing positive for Stealth Omicron.
The region had 87.9% of samples testing positive, followed by the East of England with 85.6% and the North West with 85.1%.
The North East had the lowest positivity rate in England with 71.7% of samples testing positive for Stealth Omicron.
Which authorities have the greatest number of Stealth Omicron cases?
At a local level South Bucks had the greatest proportion of tests coming back positive.
The authority had a positivity rate of 97%, followed by Rossendale which recorded 96.3% and Barrow-in-Furness with 95.9%.
Is the UKHSA concerned about Stealth Omicron?
Despite rising infections, the UKHSA said vaccination is still providing a high level of protection.
A spokesperson for the UKHSA said: “Omicron BA.2 is now the dominant variant in the UK, and has a significant growth advantage over Omicron BA.1.
“UKHSA continues to monitor all available data related to Covid-19 variants as a matter of routine, both in the UK and internationally.
“Vaccination provides a high level of protection against severe illness and it’s important that everyone has had their latest dose.
“We can all help reduce transmission by wearing a face covering in crowded or enclosed spaces, washing hands regularly and keeping rooms well ventilated.”
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