The Covid-19 mutation that originated in India – now known as the Delta variant – is now believed to be dominant in the UK, with evidence suggesting it may be more dangerous than the Kent variation.
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They are among at least 744 cases of the VOC-21APR-02 mutation in the South East – the fifth-worst affected of England's nine regions.
The North West – where variant hotspots Bolton and Blackburn are located – continues to have the highest numbers identified.
A total of 12,431 cases of the Delta variant had been confirmed in the UK by June 2, up 79% from the previous week’s total of 6,959.
Of these, 10,797 (87%) were in England, 1,511 (12%) in Scotland, 97 in Wales and 26 in Northern Ireland.
A PHE risk assessment found that vaccines were less effective against the strain compared to the Kent mutation – or Alpha variant.
The findings also suggest people are more at risk of hospital admission if infected with the Delta variant, though PHE cautioned that “more data is needed to have more confidence in that finding”.
Dr Jenny Harries, chief executive of the UK Health Security Agency, said: “With this variant now dominant across the UK, it remains vital that we all continue to exercise as much caution as possible.
“The way to tackle variants is to tackle the transmission of Covid-19 as a whole.
"Work from home where you can, and practice ‘hands, face, space, fresh air’ at all times.
“If you are eligible and have not already done so, please come forward to be vaccinated and make sure you get your second jab. It will save lives.”
PHE figures show that more than half of people found with the Indian strain were unvaccinated.
From February 1 to May 31, there were 9,427 cases of the Delta variant recorded in England, of which 5,172 were in unvaccinated people.
Of the 137 cases that resulted in a hospital admission, just seven were among people who had received both vaccine doses.
A further 24 involved patients who received their first dose more than three weeks prior, and 90 were patients who had not received any dose.
Some 17 people died over the same period with the Delta variant, of which two had received both vaccine doses and 11 were unvaccinated.
The latest PHE data also suggests there have been 97 confirmed Covid-19 outbreaks in schools that have had at least one variant case linked to them over the most recent four-week period – the equivalent of around one in 250 schools.
Professor Neil Ferguson, whose modelling was instrumental to the UK locking down in March 2020, said Prime Minister Boris Johnson faces a “very difficult” call on whether to drop restrictions on June 21.
He BBC Radio 4’s Today programme that given the “more negative direction” of the data, a cautious approach is needed as the Government balances the potential risks against a desire for normality.