NGS-SA: Network for Genomic Surveillance in South Africa

Funded by the Department of Science & Innovation (DSI) and the South African Medical Research Council (SAMRC)
to respond to the COVID-19 pandemic.

A NETWORK ESTABLISHED TO RAPIDLY RESPOND TO PUBLIC HEALTH THREATS IN SOUTH AFRICA

We are a network of laboratories, scientists and academic institutions that have joined forces to ensure the public health responses to COVID-19 in South Africa have access to the best possible scientific data. Our network was launched in June 2020 when five of the largest laboratories of the National Health Laboratory Services (NHLS) and their associated academic institutions in Bloemfontein, Cape Town, Durban, Johannesburg and Tygerberg were awarded a grant from the DSI and SAMRC. Our goal is to expand the network to also include private diagnostic laboratories and other academic institutions in South Africa and abroad.

Genomic facilities

Our genomic data is produced at five sequencing facilities in South Africa so data can be made available as quickly as possible.

Scientific researchers

We have dozens of investigators working together to analyse the data in real-time to guide public health interventions and advance academic research.

More information about members of the consortium here.
A NETWORK ESTABLISHED TO RAPIDLY RESPOND TO PUBLIC HEALTH THREATS IN SOUTH AFRICA
ALL DATA IS MADE PUBLIC AND IT IS CURATED BY AN TEAM OF AFRICAN SCIENTISTS AT GISAID

ALL DATA IS MADE PUBLIC AND IT IS CURATED BY AN TEAM OF AFRICAN SCIENTISTS AT GISAID

We have entered in a partnership with GISAID so all of our genomic data is publicly available at databases as soon as it is produced. We truly believe in fair research practices and in the need to capacitate local researchers and health care workers. We also believe that all of those involved in sampling, producing, annotating and analysing the data need to be properly acknowledged. We are working with other African networks to also train bioinformaticians so data can be also analysed quickly and accurately in Africa.

Public Data

All of our data is public but we request that you treat it as unpublished and contact us if you want to analyze and publish from it.

Data Curation & Analysis

We have also partnered with H3Africa H3AbioNet so scientists from many African countries can participate in this activity.

Learn about our public data process and download it from GISAID & GenBank

GENOMIC PROTOCOLS FOR SARS-COV-2

We have implemented open protocols for Ilumina, Oxford Nanopore Technologies and S5 Ion DNA sequencers. We have also developed two new protocols that use NEB and Nextera Flex for library preparation in Illumina. These protocols save six to nine hours of hands on time, which is important to laboratories in South Africa that lack automation. In order to allow other laboratories in the world to learn from our experience, we have made all of our protocols freely available and are training other laboratories in South Africa and abroad.

Genomic protocols

The protocols are available at Protocols.io and on our website.

Bioinformatics protocols

We produced a bioinformatics protocol on Genome Detective for all of the main sequencing platforms.

We are committed to open science and sharing all protocols
GENOMIC PROTOCOLS FOR SARS-COV-2
HIGH QUALITY DATA PRODUCED WITH GENOME DETECTIVE

HIGH QUALITY DATA PRODUCED WITH GENOME DETECTIVE

Genome Detective is an easy to use web-based software application that assembles the genomes of viruses quickly and accurately. We have fine-tuned Genome Detective to assembly high quality genomes of SARS-CoV-2. Our software is very easy to use allowing our laboratory scientists to assemble genomes as soon as they come out of the DNA sequencers.

Step by step protocol

Easy to use protocol and videos to help African researchers to assembly high-quality genomes

Training program

Training African scientists and curators to quickly assemble genomes from Illumina, Nanopore and S5 Ion platforms

Access the publication and protocols for assembly of data

UPDATES BY OUR BIOINFORMATICS TEAM

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. We do this by maintaining a section of their website that focus on the analysis of South African data. 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 data in real time can be viewed on the NGS-SA section of the Nextstrain website.

South African Datasets

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

Narratives

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

Visit our data analysis update section
UPDATES BY OUR BIOINFORMATICS TEAM