South Africa detects C.1.2 variant of interest

Recently published research has revealed that the new COVID-19 variant C.1.2 has been identified in South Africa.

According to the researchers, there are concerns that this SARS-CoV-2 variant of interest (VOI) has been associated with increased transmissibility, neutralisation resistance, and disease severity.

“Here we report the identification of a potential variant of interest assigned to the Pango Lineage C.1.2,” the preprint analysis published last week read.

The Pango, which stands for Phylogenetic Assignment of Named Global Outbreak Linages, refers to the software tool for sequence assignment used by researchers to track the transmission and spread of COVID-19.

“This lineage was first identified in May 2021 and evolved from C.1, one of the lineages that dominated the first wave of SARS-CoV-2 infections in South Africa and were last detected in January 2021.”

According to KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP) Director at the University of KwaZulu-Natal, Professor Tulio de Oliveira, this was the work of dozens of scientists as part of the Network of Genomic Surveillance in South Africa (NGS-SA).

“The preprint analysis was led by National Institute for Communicable Diseases and KRISP,” he said, adding that it also involves young women scientists, including Catherine Scheepers, who is the first author.

“The reason why we decided to publish the preprint is that we see the C.1.2 persistence in South Africa and is now in another 10 countries. It is early days as only 95 genomes have been published at GISAID. However, we found that in this pandemic, [it is crucial to] share info quicker than later,” the Professor explained.

According to the analysis, C.1.2 has since been detected across the majority of the provinces in South Africa and several other countries in Africa, Europe, Asia, and Oceania.

“The emergence of C.1.2 was associated with an increased substitution rate, as was previously observed with the emergence of the Alpha, Beta and Gamma variants of concern (VOCs).”

Variant of interest (VOI) 

The Centre for Disease Control and Prevention (CDC) defines a VOI as a variant where there is evidence of an increase in transmissibility, more severe disease, which may lead to hospitalisation or death.

The national public health agency of the United States said the significant reduction in neutralisation by antibodies generated during previous infection or vaccination, reduced effectiveness of treatments or vaccines, or diagnostic detection failures.

Meanwhile, VOCs are associated with specific genetic markers that have been associated with changes to receptor binding, reduced neutralisation by antibodies generated against previous infection or vaccination, reduced efficacy of treatments, potential diagnostic impact, or predicted increase in transmissibility or disease severity.

According to the US epidemiologist and health economist, Dr Eric Feigl-Ding, this means that this new variant has somehow mutated so fast and far that it is now the furthest mutated variant found to date.

“This C.1.2 is obviously a very fast-moving variant. We don’t know the exact transmission yet or the severity or vaccine efficacy yet. But the best advice that will serve us well is to take the precautionary principles as the approach — move fast,” he tweeted.

The Department of Health’s Deputy Director-General, Anban Pillay, told News Frame that the prevalence of the new variant in the samples that have been tested “is very low at this stage”.

“New variants are bound to develop as a natural evolution of the virus. The evidence to date indicates that the non-pharmaceutical interventions remain the key responses to these variants,” he added.

There are currently four VOCs, namely Alpha, Beta, Gamma, and Delta, and four VOIs, Eta, Iota, Kappa, and Lambda in circulation globally.