Tracking the emergence of new SARS-CoV-2 variants in South Africa

Summary: The study identified 16 new lineages of SARS-CoV-2 in South Africa between March and August 2020, with unique mutations not found elsewhere. Three lineages (B.1.1.54, B.1.1.56, and C.1) dominated during the country's first wave, accounting for approximately 42% of all infections. The C.1 lineage, with 16 nucleotide mutations including the D614G spike protein change, became the most geographically widespread by August 2020. Genomic surveillance played a crucial role in identifying the 501Y.V2 variant in South Africa in December 2020.