Johannesburg: South Africa has identified a potential Variant of Interest (VOI) of Covid-19 that is assigned to the PANGO lineage C.1.2. The variant, first identified in May 2021 during the third wave of Covid in the country, has since been detected across the majority of the provinces in South Africa and in seven other countries spanning Africa, Europe, Asia, and Oceania, researchers at the National Institute for Communicable Diseases (NICD) and the KwaZulu-Natal Research Innovation and Sequencing Platform said in their report.
The study is yet to be peer-reviewed and is posted on the pre-print server medRxiv. Meanwhile, India has also reported the presence of a new sub-lineage AY.12 of the Delta variant, which 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.
The Covid 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.
The potential Variant of Interest has 41.8 mutations per year, according to the study. 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. The study also showed 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, 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.
(With Inputs from IANS)
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