In this article the authors describe a new SARS-CoV-2 lineage (501Y.V2) characterized by eight lineage-defining mutations in the spike protein, including three at important residues in the receptor-binding domain (K417N, E484K and N501Y) that may have functional significance. This lineage was identified in South Africa after the first epidemic wave in a severely affected metropolitan area, Nelson Mandela Bay, located on the coast of the Eastern Cape Province. This lineage spread rapidly, becoming dominant in the Eastern Cape, Western Cape and KwaZulu-Natal Provinces within weeks. Whilst the full significance of the mutations is yet to be determined, the genomic data, showing the rapid expansion and displacement of other lineages in multiple regions, suggest that this lineage is associated with a selection advantage, most plausibly as a result of increased transmissibility or immune escape.
Tegally, H., Wilkinson, E., Giovanetti, M. et al. Emergence of a SARS-CoV-2 variant of concern with mutations in spike glycoprotein. Nature (2021). https://doi.org/10.1038/s41586-021-03402-9