The government-run National Institute for Communicable Diseases (NICD) said 22 positive cases of the B.1.1.529 variant have been recorded in the country following genomic sequencing.
It said in a statement Thursday that detected cases and the percentage testing positive are "increasing quickly" in three of the country's provinces including Gauteng, which includes Johannesburg and Pretoria.
A cluster outbreak was recently identified, concentrated at a higher education institute in the capital Pretoria, the NICD said.
Last year South Africa also detected the Beta variant of the virus, although until now its infection numbers have been driven by the Delta variant, which was originally detected in India.
The country has the highest pandemic numbers in Africa with around 2.95 million cases, of which 89,657 have been fatal.
- Ten mutations -
Scientists said the new B.1.1.529 variant has at least 10 mutations, compared to two for Delta or three for Beta.
"What gives us some concerns (is) that this variant might have not just have enhanced transmissibility, so spread more efficiently, but might also be able to get around parts of the immune system and the protection we have in our immune system," said researcher Richard Lessells.
So far the variant has been seen spreading especially among young people.
But the coming days and weeks will be key to determine the severity of the variant, Lessells said.
Neutralising the variant is "complicated by the number of mutations this variant" contains, said one of the scientists Penny Moore.
"This variant contains many mutations that we are not familiar with," she added.
After a rather slow start to South Africa's vaccination campaign, around 41 percent of adults have received at least a single dose, while 35 percent are fully vaccinated.