South Africa has identified a potential variant of interest (VOI) of Covid-19 that is assigned to the PANGO lineage C.1.2. C.1.2 was first identified in May 2021 during the third wave of Covid in the country, said researchers from the country’s National Institute for Communicable Diseases (NICD) and the KwaZulu-Natal Research Innovation and Sequencing Platform.
It has since been detected across the majority of the provinces in South Africa and in seven other countries spanning Africa, Europe, Asia and Oceania, the researchers reported in the study that is yet to be peer-reviewed and is posted on pre-print server medRxiv.
The variant has evolved from C.1, one of the lineages that dominated the first wave of SARS-CoV-2 infections in South Africa and was last detected in January 2021. C.1.2 is “associated with increased transmissibility and reduced neutralisation sensitivity,” wrote the team, including Cathrine Scheepers, from NICD, in the abstract.
Compared to C.1, the new variant has “mutated substantially” and is more mutations away from the original virus detected in Wuhan than any other Variant of Concern (VOC) or VOI detected so far worldwide.
According to the study, 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.
A similar short period of increased evolution was also associated with the emergence of the Alpha, Beta, and Gamma VOCs, said the researchers, suggesting that a single event, followed by the amplification of cases, drove a faster mutation rate.
About 52 per cent 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.
Further, the study also found consistent increases in the number of C.1.2 genomes in South Africa on a monthly basis, rising from 0.2 per cent in May to 1.6 per cent in June and 2.0 per cent in July. The researchers stated that it is similar to the increases seen in Beta and Delta in South Africa during early detection.
As of August 20, 2021, 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).
More study is needed “to determine the functional impact of these mutations, which likely include neutralising antibody escape, and to investigate whether it confers advantage over the Delta variant,” Scheepers said.
Meanwhile, India has also reported the presence of a new sub-lineage AY.12 of the Delta variant of Covid, that was recently classified in Israel. A recent report by the Indian SARS-CoV-2 Genomics Consortium (INSACOG), many cases in India that were earlier classified as Delta, are now being reclassified as AY.12.
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