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

Early transmission of SARS-CoV-2 in South Africa: An epidemiological and phylogenetic report

Authors: Giandhari J, Pillay S, Wilkinson E, Tegally H, Sinayskiy I, Schuld M, Lourenšo J, Chimukangara B, Lessells R, Moosa Y, Gazy I, Fish M, Singh L, Khanyile KS, Fonseca V, Giovanetti M, Alcantara LCJ, Petruccione F, de Oliveira T

Journal: IJID, 2020. DOI:



To investigate introduction and understand the early transmission dynamics of the SARS-CoV- 2 in South-Africa, we formed the Network for Genomic Surveillance in South Africa (NGSSA)


Here, we present the first results of this effort, which is a molecular epidemiological study of the first twenty-one SARS-CoV-2 whole genomes sampled in the first port of entry, KwaZulu- Natal (KZN), during the first month of the epidemic. By combining this with calculations of the effective reproduction number (R), we aim to shed light on the patterns of infections in South Africa.


Two of the largest provinces, Gauteng and KwaZulu-Natal, had a slow growth rate on the number of detected cases, while in Western Cape and Eastern Cape the epidemic is spreading fast. Our estimates of transmission potential suggest a decrease towards R=1 since the first cases and deaths but a subsequent estimated R average of 1.39 between 6-18th of May 2020. We also demonstrate that early transmission in KZN was associated with multiple international introductions and dominated by lineages B1 and B and provide evidence for locally acquired infections in a hospital in Durban within the first month of the epidemic.


The COVID-19 pandemic in South Africa was very heterogeneous in its spatial dimension, with many distinct introductions of SARS-CoV2 in KZN and evidence of nosocomial transmission, which inflated early mortality in KZN. The pandemic at the local level is still developing and the objective of NGS-SA is to clarify the dynamics of the epidemic in South Africa and devise the most effective measures as the outbreak evolves.