The C.1.2 strain, which is linked to 'increased transmissibility', is more mutations away from the original virus seen in Wuhan, experts at South Africa's National Institute for Communicable Diseases and the KwaZulu-Natal Research Innovation and Sequencing Platform said.
The virus was first identified by scientists in South Africa in May and has since been found in England, China, the Democratic Republic of the Congo, Mauritius, New Zealand, Portugal and Switzerland.
In their study, scientists found the strain, which descends from the C.1 strain that was first spotted amid the first wave of the pandemic, has a mutation rate of approximately 41.8 mutations per year.
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This rate is nearly double the current global mutation rate seen in any other Variant of Concern (VOC) thus far.
During their study, researchers found a monthly increase in the number of C.1.2 genomes in South Africa, rising from 0.2 per cent in May to 1.6 per cent in June and 2.0 per cent in July.
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This short period of consistent increase has also been spotted in the Alpha, Beta and Gamma variants.
Scientists also found 14 mutations in nearly 50 per cent of the variants which had a C.1.2 sequence.
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While more research is required 'to determine the functional impact of these mutations', scientists warned the latest variant, which has 'mutated substantially', could help the virus evade antibodies and immune responses.
In their report, which was published in the journal Nature, the scientists concluded: 'We describe and characterise a newly identified SARS-CoV-2 lineage with several spike mutations that is likely to have emerged in a major metropolitan area in South Africa after the first wave of the epidemic, and then to have spread to multiple locations within two neighbouring provinces.
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``We show that this lineage has rapidly expanded and become dominant in three provinces, at the same time as there has been a rapid resurgence in infections.
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'Although the full import of the mutations is not yet clear, the genomic and epidemiological data suggest that this variant has a selective advantage—from increased transmissibility, immune escape or both.
'These data highlight the urgent need to refocus the public health response in South Africa on driving transmission down to low levels, not only to reduce hospitalisations and deaths but also to limit the spread of this lineage and the further evolution of the virus.'
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Earlier this month, a report published by Public Health England declared that the C.1.2 strain was among ten variants being monitored by scientists in the UK.
Scientists working on a Tel Aviv University study reported that their results suggested the vaccine is less effective against the South African variant - compared with the original coronavirus and the Kent variant.
The alterations open the door to it being resistant to vaccines, which train the body to spot the spike protein, or natural immunity from previous infection.
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