NGS-SA: Network for Genomic Surveillance in South Africa YouTube Lecture Handouts

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NGS-SA: Network for Genomic Surveillance in South Africa | Leads in Strain Detection for SARS COV 2

NGS-SA

  • Established: June 2020
  • Funding: Department of Science & Innovation (DSI) and the South African Medical Research Council (SAMRC)
  • Partners: H3Africa H3AbioNet
  • Funded by the Department of Science & Innovation (DSI) and the South African Medical Research Council (SAMRC) to respond to the COVID-19 pandemic.
  • 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.
  • The goal of this project is create H3ABioNet, a pan-African bioinformatics network. At the outset, H3ABioNet will include nodes of computational expertise in more than 15 African countries. H3ABioNet will provide a framework for integration of and communication among all of the H3Africa research and resource projects, as well as other sites in Africa that are carrying out genomic/genetic research
  • H3ABioNet is a pan-African network consisting of 28 nodes across 16 African countries.

= Lead Institution

South Africa: University of Cape Town

Non-African Collaborators

USA: University of Illinois

  • The Human Heredity and Health in Africa (H3Africa) consortium facilitates fundamental research into diseases on the African continent while also developing infrastructure, resources, training, and ethical guidelines to support a sustainable African research enterprise – led by African scientists, for the African people.
  • The initiative consists of 51 African projects that include population-based genomic studies of common, non-communicable disorders such as heart and renal disease, as well as communicable diseases such as tuberculosis.
  • These studies are led by African scientists and use genetic, clinical, and epidemiologic methods to identify hereditary and environmental contributions to health and disease.

NGS-SA Members

  • NHLS Tygerberg Hospital, Stellenbosch University (SU)
  • NHLS Groote Schuur Hospital, University of Cape Town (UCT)
  • NHLS Universitas Academic Laboratories, University of The Free State (UFS)
  • NHLS Inkosi Albert Luthuli Central Hospital (Ialch) , University of Kwazulu-natal (UKZN)
  • National Institute for Communicable Diseases (NICD)
  • KRISP: KZN Research Innovation & Sequencing Platoform, University of Kwazulu-natal
  • Computational Biology Division at The University of Cape Town (UCT)
  • South African National Bioinformatics Institute (SANBI)
  • Center For Quantum Technology at University of Kwazulu-natal
  • Department Of Medical Virology, Zoonotic Arbo and Respiratory Virus Research Programme (ZARV)
  • NHLS, Tshwane Academic Division (NHLS-TAD) , University of Pretoria (UP)

Principles

  • Sequencing close to sample collection
  • Being platform agnostic
  • Supporting locally relevant public health priorities, such as by controlling clusters of outbreaks
  • Ensuring rapid and responsible open data sharing
  • Creating a bioinformatics system to process and analyses data locally
  • Producing timely reports to inform policy makers.

Genomic Protocols

  • Ilumina
  • Oxford Nanopore Technologies
  • S5 Ion DNA sequencers
  • NEB
  • Nextera Flex
  • NGS-SA 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
  • 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.
  • 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.
  • Nextstrain is an open-source project to harness the scientific and public health potential of pathogen genome data. We provide a continually-updated view of publicly available data alongside powerful analytic and visualization tools for use by the community. Our goal is to aid epidemiological understanding and improve outbreak response

Mayank