The rise in daily infections, which had eased in the last few months with reports of daily new cases between 1,000 and 2,000 till mid-November, reached 8,725 with 274 deaths, the health ministry said in a statement.
South Africa has recorded the highest number of coronavirus infections in Africa, approaching the 900,000 mark, with over 20,000 related deaths.
This genomics team, led by the Kwazulu-Natal Research Innovation and Sequencing Platform has sequenced hundreds of samples from across the country since the beginning of the pandemic in March.
Health Minister Zweli Mkhize said at a briefing that anecdotal evidence suggests a shift in the clinical epidemiological picture whereby more younger patients are presenting with critical illness.
He said the virus was "spreading faster than the first wave" and was "probably across most of SA by now".
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He also added that scientists do not know where the new variant originated but that the country was seeing a much higher proportion than the rest of the world.
The result, it's now clear, that South Africa's teenagers are driving a second wave of infections. "Once we've grown the virus, we will add in convalescence serum from those patients who recovered from the virus in the first wave to see whether it neutralises the virus", Prof Karim said.
"We had all of these different strains routinely spreading in South Africa during our first wave and subsequently".
He said people should be concerned about this new variant of the virus, but there was no reason to panic. These mutations were not seen in new variants in the United Kingdom and Australia.
Unlike in the United Kingdom and Australia, where their new variants are uncommon, South Africa's 501.V2 variant is widespread, and experts say it's driving the concerning second Covid-19 wave in South Africa. Friday's milestone comes just after 15 days, that is December 3, when the country crossed the 800,000 mark in daily infections.