It has mutations likely to evade the immune response generated by prior infection and vaccination, and also mutations associated with increased infectivity.
Lab studies are needed to assess the likelihood of the mutations resulting in greatly reduced vaccine efficacy, scientists said.
Officials advised the government on the need to act swiftly and pre-emptively in case the concerns over the affect of the variant are borne out, even though it could take weeks to generate all the information needed about its characteristics.
Earlier on Thursday, SA scientists said they had detected the new Covid-19 variant in small numbers and were working to understand its potential implications.
The variant has a “very unusual constellation” of mutations, which is concerning because they could help it evade the body's immune response and make it more transmissible, the scientists told reporters at a news conference.
The variant has also been found in Botswana and Hong Kong.
The UK Health Security Agency said no cases of the variant had been detected in Britain and they were in contact with SA colleagues about their data.