Possible cluster of viral COVID variants from South Africa under the microscope

By Melissa Coade

Wednesday September 1, 2021

C.1.2, a new potential cluster of viral COVID variants first detected in South Africa, has accumulated a high number of mutations
C.1.2, a new potential cluster of viral COVID variants first detected in South Africa, has accumulated a high number of mutations. (ink drop/Adobe)

C.1.2, a new potential cluster of viral COVID variants first detected in South Africa in May, has accumulated a high number of mutations according to the National Health Laboratory Service (NHLS) in South Africa.

Scientists from the KwaZulu-Natal Research and Innovation and Sequencing Platform believe that the number of mutations undergone by C.1.2 exceed the mutations that have been identified in all four COVID-19 variants of concern (Alpha, Beta, Delta and Gamma).

The findings have been shared In a preprint of a recent study, which has not been peer-reviewed, suggesting that C.1.2 has more immune evasion properties than the highly virulent Delta variant. 

Monash University Malaysia’s Dr Vinod Balasubramaniam said C.1.2 mutated twice as fast as other global variants.

“It is between 44 and 59 mutations away from the original virus detected in Wuhan, making it more mutated than any other WHO-identified variant of concern (VOC),” Balasubramaniam said. 

“It also contains many mutations which have been associated with increased transmissibility and a heightened ability to evade antibodies in other variants, the scientists said, though they occur in different mixes and their impacts on the virus are not yet fully known.”

The World Health Organisation is yet to classify the potential cluster as a variant of interest (VOI), which is the official step before it becomes classified as a VOC.

In South Africa where genome sequencing of positive COVID cases has increased, C.1.2 has comprised 2% of the known COVID-19 variants spread in that country. Most infections in South Africa at present result from the Delta variant, which was first detected in India. But C.1.2 has also been detected in seven other countries, including New Zealand, with about 100 sequences of the viral cluster detected since it was discovered three months ago.

According to clinical virologist Associate Professor Ian Mackay, the SARS-CoV-2 virus (which caused the COVID-19 pandemic) has continued to mutate as it spreads ‘freely and continuously’ among humans. He said that without knowing more about it, there is no current indication that the viral cluster should be an ‘urgent cause of concern’.

“The study describes this viral variant’s genetic features but doesn’t give us new evidence about signs and symptoms of COVID-19, the incubation period, serial interval, viral load, transmission efficiency, immune response or ongoing vaccine effectiveness,” Mckay said.

“We do know the viruses harbour some mutations that may be a cause for concern when viewed individually. How the constellation of mutations interacts in the final viral package and once in humans though, is unclear.”

Mackay, who works at the University of Queensland, said the best thing people could do to protect themselves from getting infected by any SARS-CoV-2 variant was to get vaccinated, wear a mask in crowded places, and socially distance.

“We [can] work hard to avoid sharing the same air as those who might be infected. All of these steps combine to help keep us as safe as we can be from this latest airborne virus,” Mackay said. 

Increasing vaccination rates in Australia should remain a top priority according to the University of Sydney’s Professor Sarah Palmer, who is the co-director of the Centre for Virus Research and the Westmead Institute for Medical Research. 

“This current finding of a new variant that may be more infectious than the Delta variant underscores that we must increase our vaccination rates here in Australia and globally. The race continues between vaccines and variants,” Palmer said. 

As for how concerning this new development is, Balasubramaniam says it was to be expected that new COVID variants would develop and with more mutations over the course of the pandemic. 

“The full extent of the fitness and pathogenicity of the new variant is still very much under review.”

“C.1.2 still makes up a very small but consistently growing portion of all of South Africa’s cases. It accounted for just 1% of samples in June and 3% in July, versus 67% of samples in June and 89% in July for the delta variant,” Balasubramaniam said.


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