New potential COVID-19 variant of concern identified in South Africa

In South Africa, a new potential COVID-19 variant of interest (VOI) has been identified.

Scientists from the KwaZulu-Natal Research Innovation and Sequencing Platform and the National Institute for Communicable Diseases (NICD) of South Africa first spotted the strain in May 2021 during the third wave of Covid in the country. 

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Since then, the strain which has been assigned to the PANGO lineage C.1.2, has been detected in most of South Africa's provinces as well as in seven other countries across Africa, Europe, Asia and Oceania.

The variant is believed to have evolved from C.1, one of the lineages predominant during the first outbreak of SARS-CoV-2 in South Africa.

According to the study's abstract C.1.2 is associated with reduced neutralisation sensitivity, as well as having increased transmissibility.

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Compared to C.1, the new variant has undergone substantial mutations and is further away from the original virus detected in Wuhan than any other variant of concern (VOC) or VOI detected so far around the world.

Study results indicate that C.1.2 develops 41.8 mutations per year. This is an approximately 1.7-fold increase over the current global rate and an approximately 1.8-fold increase over the original SARS-CoV-2 evolution estimate.

Alpha, Beta, and Gamma VOCs also emerged after a similarly short period of increased evolution. The researchers suggest that one event, followed by amplification in the number of cases, was responsible for the faster mutation rate.

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Over half or 52 per cent of the spike mutations identified in C.1.2 have already been identified in other VOIs and VOCs.

Moreover, the study found a consistent rise in the number of C.1.2 genomes each month in South Africa, rising from 0.2 per cent in May to 1.6 per cent in June and 2.0 per cent in July. Researchers noted this is similar to what was observed in Beta and Delta during early detection in South Africa.

80 sequences matching the C.1.2 lineage are already listed on the open-access database GISAID (Global Initiative on Sharing Avian Influenza Data) as of August 20, 2021.

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," says Cathrine Scheepers, from NICD.

These findings have been reported in a study that has yet to be peer-reviewed but is available on the medRxiv server.

(With inputs from agencies)