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Health Secretary Matt Hancock says a new variant of Covid has been discovered in Kent.
It is thought to explain the reason for soaring rates across the county.
According to Sky News it was first discovered during routine surveillance by Public Health England. Ministers were told about it on Friday.
The news came as it was confirmed London would be plunged into Tier 3, with the Government deciding it could not wait for the planned review later this week.
It has also been revealed that parts of Essex will be put into Tier 3 while others remain in Tier 2 - in stark contrast to neighbouring Kent which was treated as a single area when it was put under the toughest restrictions.
Mr Hancock said that scientists had identified a 'new variant' of the virus that appeared to be influencing the spread in the south of England.
But he stressed that it did not seem to be more deadly, and there was likely to be low risk that it will not respond to vaccines.
"We have identified a new variant of coronavirus, which may be associated with the fastest spread in the south-east of England," Mr Hancock said.
"Initial analysis suggests that this variant is growing faster than the existing variants. We’ve currently identified over 1,000 cases with this variant, predominantly in the south of England, although cases have been identified in nearly 60 different local authority areas, and numbers are increasing rapidly."
Medway has the second worst rate of coronavirus infection in England, second only to neighbouring Swale. The latest government data shows a rate of 604.9 cases per 100,000 people in the Towns, an increase of 1.4% in new cases week-on-week.
The news London was being placed into Tier 3 followed warnings from London Mayor Sadiq Khan that the Tier 3 restrictions – which will involve the closure of pubs and restaurants except for takeaway and delivery services – would have a “catastrophic” economic impact.
Mr Khan had suggested closing schools in the capital early for the Christmas break and returning later in January in an effort to curb the spread of the virus.