Cyril Ramaphosa started feeling unwell on Sunday and has delegated all responsibilities to his deputy.
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South Africa President Cyril Ramaphosa is receiving treatment after testing positive for Covid-19, his office says.
In a statement, it says the 69-year-old has mild symptoms and is isolating in Cape Town.
South Africa has seen a surge of infections since the new Omicron variant was first detected in November.
Despite Omicron being more transmissible than previous strains, including Delta, risk of severe disease and death is low, a study has found.
South Africa’s presidency says Mr Ramaphosa tested positive on Sunday, and has already delegated all responsibilities to Deputy President David Mabuza “for the next week”.
The statement says the president started feeling unwell after attending the funeral of former President FW de Klerk early on Sunday.
It adds that Mr Ramaphosa is in “good spirits” – but is being monitored by doctors.
The statement provided no further details about Mr Ramaphosa’s infection.
Mr Ramaphosa had recently returned from a seven-day tour of Nigeria, Ivory Coast, Ghana and Senegal.
Some members of his delegation had tested positive in Nigeria and returned directly to South Africa, reports the BBC’s Nomsa Maseko in Johannesburg.
The presidency says Mr Ramaphosa, who was vaccinated in February, and members of his team were tested for Covid in all countries they visited.
The president says his own infection should serve as a caution to people to observe public health measures as well as get vaccinated.
Despite very public pleas from the authorities, fewer than 30% of South Africans are fully vaccinated because of what the country’s health authorities describe as a mass “vaccine hesitancy”.
South African scientists alerted the World Health Organization about the new Omicron variant on 24 November.
The UN public health body later classed Omicron as “a variant of concern”, warning that vaccines against it may be less effective.
A number of countries around the world have since introduced travel bans against South Africa and several neighbouring countries – but this has failed to stop the spreading of the new variant.
A recent study has found that Omicron is “antibody evasive” against people who have been vaccinated and those with prior infections.
“We are seeing a large number of breakthrough infections… but those infections are not progressing to severe disease or death in any sort of meaningful large numbers,” said Shabir Madhi, vaccinology professor at Johannesburg’s University of the Witwatersrand.
“As an example yesterday [Sunday] there were about 20,000 cases reported and about 25 people who died of Covid-19,” he told the BBC’s Newsday programme.
“During the course of the Delta variant wave, when there were 20,000 cases in South Africa the number of those dying each day was between 200 and 300,” Prof Madhi said.
He added that even though testing was low in South Africa, experts did not expect the number of deaths to come “anywhere close” to the fatalities recorded in the previous three waves.