NGS-SA: Publications and pre-prints of our genomics surveillance work

Accelerating genomics-based surveillance for COVID-19 response in Africa

Authors: Tessema SK, Inzaule SC, Christoffels A, Kebede Y, de Oliveira T, Ouma AEO, Happi CT, Nkengasong JN

Journal: Lancet Microbe, 2020. DOI:


Timely sequencing of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) coupled with rapid data sharing has allowed researchers to develop counter-measures against the virus such as diagnostic tests and vaccines,1 and assess transmission and evolution dynamics as the virus spreads globally. Despite the minimal resources available in the African continent, local experts have risen to the challenge and adopted genomics-based surveillance to guide the outbreak response.

As of June 19, 2020, a total of 568 SARS-CoV-2 genome sequences had been shared from 12 African countries and are providing insight into the ongoing epidemiology of the virus. Early findings from genome sequencing have shown that SARS-CoV-2 strains circulating in Africa are assigned to 20 imported lineages, ranging from three lineages in Nigeria to ten in Kenya.

The majority of the SARS-CoV-2 sequences are of B.1 (65%) and B.1.1 (15%) lineages, which are thought to be predominantly of European origin (appendix). The next most predominant lineage was A (5%), which originated in China. Therefore, sequencing has revealed that multiple lineages have been introduced into the continent.