Epidemiology: Sixteen new SARS-CoV-2 lineages spread through South Africa from March to August 2020

An analysis of more than 1,300 near-whole genome sequences of SARS-CoV-2 isolated in South Africa during the first 6 months of the pandemic revealed 16 new lineages of the virus. These findings, reported in a paper published in Nature Medicine, shed light on the spread of SARS-CoV-2 throughout South Africa from 6 March to 26 August 2020.

The COVID-19 pandemic in South Africa is the largest in Africa, with more than 785,000 people infected (which accounted for approximately 50% of all known African infections) and more than 20,000 deaths by the end of November 2020.

Genomic epidemiology has been used to understand the evolution of SARS-CoV-2 and to track the dynamics of transmission across the world. Houriiyah Tegally, Tulio de Oliveira and colleagues analyzed 1,365 near-whole genomes of SARS-CoV-2 collected in South Africa during the first 6 months of the pandemic and identified 16 new lineages. Most of these lineages have unique mutations that have not been identified elsewhere. The authors found that three of these lineages—B.1.1.54, B.1.1.56 and C.1—spread widely in South Africa during the first wave, accounting for around 42% of all infections in the country at the time. The newly identified C lineage of SARS-CoV-2, C.1, was the most geographically widespread lineage in South Africa by the end of August 2020.

The authors conclude that this type of genomic surveillance can be used on a large scale in Africa to identify new lineages of SARS-CoV-2 and to inform measures to control the spread of the virus. Such genomic surveillance was crucial in the identification of the 501Y.V2 variant in South Africa in December 2020.