Spatial and Genomic monitoring of COVID-19 cases in South Africa in order to fight the flames before they become a wild fire.. NHLS-UCT-Virology-wgs-SARS-Cov-2

The Network for Genomics Surveillance in South Africa (NGS-SA), supported by the South African Medical Research Council (SAMRC) and the Department of Science and Innovation (DSI), has been conducting genomic surveillance on the SARS-CoV-2 epidemic in South Africa. We have produced over 3,000 genomes, which are publicly available at GISAID. This has informed an understanding of the introduction and early spread of SARS-CoV-2 in South Africa, and we have identified a number of SARS-CoV-2 lineages that are unique to South Africa. In response to the resurgence of COVID-19 in the Eastern Cape since October, and in response to concerns raised by teams directly involved in the COVID-19 response in Eastern Cape (including Netcare management), we enriched our normal sampling for the genomic surveillance with additional samples from Eastern Cape. The main objective was to help understand why there might have been such a dramatic resurgence in Eastern Cape associated with high mortality.