South Africa has identified a new potential ‘Variant of Concern’ of the COVID-19 causing coronavirus. The new variant is assigned to the PANGO lineage C.1.2, said a report by the researchers at the National Institute for Communicable Diseases (NICD) and the KwaZulu-Natal Research Innovation and Sequencing Platform.

The new variant, C.1.2 was first identified in May, when the country was reeling with the third wave of COVID-19. Since then, this variant has been detected in almost all major provinces and in seven other countries in Africa, Asia, Europe, Oceania. The study is yet to be peer-reviewed.

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According to the report, C.1.2 is linked with increased transmissibility and reduced neutralisation sensitivity” and has mutated substantially than its parent lineage.

More study is needed “to determine the functional impact of these mutations, which likely include neutralising antibody escape, and to investigate whether it confers an advantage over the Delta variant,” one of the authors of the report said.

The variant, which is believed to be evolved from the C.1 lineage,  is more mutations away from the original virus detected in Wuhan than any other Variant of Concern (VOC) or VOI detected so far worldwide.

C.1 variant was responsible for the first deadly wave of coronavirus in South Africa. The variant was last detected in January 2021. 

According to the study, the new C.1.2 has 41.8 mutations per year. It is approximately 1.7-fold faster than the current global rate and 1.8-fold faster than the initial estimate of SARS-CoV-2 evolution.

The C.1.2 variant is said to have many similarities with the other variants of concerns- Alpha, Beta and Gamma. A similar short period of evolution is seen in this variant as well.

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About 52% of the spike mutations identified in C.1.2 have previously been identified in other VOIs and VOCs. These include D614G, common to all variants, and E484K and N501Y which are shared with Beta and Gamma, with E484K also seen in Eta and N501Y in Alpha, the report noted.

Consistent increases in the number of C.1.2 genomes in South Africa have been found on a monthly basis, rising from 0.2% in May to 1.6% in June and about 2% in July. The researchers stated that it is similar to the increases seen in Beta and Delta in South Africa during early detection.

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Delta variant, first detected in India, was called the ‘fittest and fastest’ variant of the coronavirus by scientists.

Coming back to the new variant, about 80 sequences that match the C.1.2 lineage have been listed on the open-access database GISAID (Global Initiative on Sharing Avian Influenza Data) as of August 8, 2021.