NGS-SA: Updates, COVID-19 analysis, narratives, reports

NGS-SA are committed to open science and sharing all updates as rapidly as possible but believe that research should be fair.
Please note that the updates shared is the work of hundreds of people and must be treated as unpublished updates.
If you wish to analyse the updates and publish research, pleasee contact NGS-SA to ensure that those who have generated the updates can be involved.

NGS-SA updates are informing the public health response in South Africa

Informing the public health response in South Africa

Our work is already influencing policy and practice in South Africa. For example, the report of our genomic analysis of the large nosocomial outbreak has been used to advise health facilities across the country on how to strengthen infection prevention and control systems. This was particularly important in South Africa, which had no experience from the previous coronavirus pandemics. We shared the report openly and disseminated the lessons learnt throughout local, regional and national health care worker networks. We believe that, even though we will not have the resources to sequence every SARS-CoV-2 genome in the country, targeted rational use of genome sequencing can be a vital resource to support the epidemic response.

Public Updates

All of our updates is public but we request that you treat it as unpublished and contact us if you want to analyze and publish from it.

Analyses Updates

We believe that open access results is crucial to facilitate a rapid response to the COVID-19 pandemic.

Access Updates


We have partnered with Nextstrain and have a team of bioinformaticians in South Africa that use their platform to continuously analyse SARS-CoV-2 lineages circulating in the country. Our goal is to develop greater epidemiological understanding of the virus and to improve quick outbreak response to COVID-19 in South Africa. Visualization and analysis of the South African updates in real time can be viewed on the NGS-SA section of the Nextstrain website.


Our Updates are continuously updated and phylogenetic trees presented with genomic mutations of SARS-CoV-2 on Nextstrain.


We are also producing narrative reports, which show how SARS-CoV-2 was introduced to and is being transmitted in South Africa.