Alliance for Pandemic Preparedness

February 3, 2021

Sixteen Novel Lineages of SARS-CoV-2 in South Africa



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An analysis of 1,365 SARS-CoV-2 genomic sequences in South Africa identified 16 new lineages of the virus isolated between March 6 and August 26, 2020. Three lineages (B.1.1.54, B.1.1.56 and C.1) were responsible for 42% of all infections in South Africa during the first wave, during which 42 detectable lineages were circulating throughout the country. By the end of August, the C.1 lineage was the most geographically widespread, while an earlier B.1.106 (identified in April, 2020) became extinct after outbreaks were contained. The authors suggest that the rapid spread of some lineages may have been due to outbreaks rather than enhanced fitness.

Tegally et al. (Feb 2, 2021). Sixteen Novel Lineages of SARS-CoV-2 in South Africa. Nature Medicine.