Epidemiology: Analysis of a SARS-CoV-2 variant in South Africa

A new SARS-CoV-2 variant that rapidly became dominant in parts of South Africa towards the end of 2020 may have emerged from the coast of the Eastern Cape Province after the first wave of the epidemic, suggests a study published in Nature today. The rapid displacement of other SARS-CoV-2 lineages in multiple regions indicates that this variant has an advantage over these other strains, possibly owing to increased transmissibility and/or escape of the immune system.

The second wave of the SARS-CoV-2 epidemic in South Africa began around October 2020 and was notably rapid in parts of the Eastern Cape, Western Cape and KwaZulu-Natal Provinces, prompting an intensification of genomic surveillance. A new SARS-CoV-2 variant (named 501Y.V2 / B.1.351) was identified by the Network of Genomic Surveillance in South Africa (NGS-SA), Tulio de Oliveira and colleagues through the analysis of 2,882 SARS-CoV-2 whole genomes from South Africa collected between 5 March and 10 December 2020. Their data suggest that the new variant emerged around August 2020 in Nelson Mandela Bay, becoming the dominant lineage in the Eastern Cape, Western Cape and KwaZulu-Natal Provinces by the end of 2020.

The 501Y.V2 variant is defined by eight mutations in its spike protein, which mediates cell entry. One of these mutations, N501Y, is also present in a variant identified in the UK (B.1.1.7), and is associated with enhanced binding to the human ACE2 receptor. Another mutation, E484K, has been associated with resistance to neutralizing antibodies. The distribution and spread of 501Y.V2, along with insights from genomic analysis, suggest that the variant may be more transmissible than other SARS-CoV-2 lineages. However, the full import of the mutations is not yet clear and requires further study, the authors conclude.

The paper is available at the following link: https://www.nature.com/articles/s41586-021-03402-9