Everyone living in the SE5 postcode in Southwark and parts of Harrow with HA2 and HA3 postcodes are being encouraged to get a test when offered, even if they are not showing symptoms.
Anyone who tests positive for the variant will go through enhanced contact tracing, the Department of Health said.
Scientists fear the strain, which is thought to be 1.5 times more transmissible, could be more resistant to existing Covid vaccines.
The Department of Health said in a statement: “Further targeted areas will have additional testing made available to control and suppress the potential spread of the Covid-19 variant first identified in South Africa.
“Working in partnership with the local authority, additional testing and genomic sequencing is being deployed to a highly targeted area within Southwark (SE5) and in parts of Harrow (HA2 and HA3), where the Covid-19 variant first identified in South Africa has been found.
“The increased testing is being introduced in addition to existing extensive testing and, in combination with the public following current lockdown rules and Hands Face Space advice, will help to monitor and suppress the spread of the virus.”
It came as pharmaceutical company AstraZeneca insisted that its Covid vaccine was safe, after concern around blood clots prompted Ireland to become the latest European country to suspend use of the jabs.
A review of available safety data in more than 17 million people who have been vaccinated across the UK and EU has shown no evidence of an increased risk, the pharmaceutical giant said.
People across the UK are still being urged to get their vaccine.
The number of cases of blood clots reported is lower than the hundreds of cases that would be expected among the general population, AstraZeneca’s chief medical officer Ann Taylor said.
The statement came after Irish Minister for Health Stephen Donnelly said on Sunday that use of the Oxford/AstraZeneca jab was being temporarily suspended as a “precautionary step”.
The decision followed reports of serious clotting in adults in Norway which left four people in hospital.
Several other European countries have temporarily suspended use of the Oxford/AstraZeneca jabs.
Additional reporting by PA