NGA-SA: Network members: NHLS, NICD, UCT, UKZN, Stellenbosch, SANBI, H3AbioNet and others

We are a network of laboratories, scientists and academic institutions who rapidly respond to public health threats.
For COVID-19, samples are processed and diagnosed at NHLS and private laboratories.
Samples are sequenced in genomic facilities across South Africa.
More detailed information about us below.

THE DIVISION OF MEDICAL VIROLOGY AT NHLS TYGERBERG HOSPITAL, STELLENBOSCH UNIVERSITY (SU)

Tygerberg Hospital at the University of Stellenbosch has a well-equipped Virology Diagnostic laboratory, which forms part of the NHLS, Tygerberg Business Unit and Coastal Branch. The Diagnostic Laboratory is accredited by the South African National Accreditation System (SANAS) with ISO 15198, July 2002. This laboratory renders a clinical diagnostic service to Tygerberg Academic Hospital (TBH) and the secondary hospitals and primary clinics of the surrounding areas. It has state-of-the-art laboratory equipment with Oxford Nanopore Technologies (ONT) with MinION and GridION X5 electronic sequencers. It also has a cryolaboratory employing advanced, standardized procedures for processing and storing patient samples, and a fully functional biosafety level 3 (BSL3) laboratory suite.

Stellenbosch Team

The diagnostic team is well integrated with the research and clinical teams. They are supported by the genomics team, who produce data on site.

Stellenbosch Investigators

- Prof. Susan Engelbrecht
- Prof. Gert Van Zyl
- Prof. Wolfgang Preiser

THE DIVISION OF MEDICAL VIROLOGY AT NHLS TYGERBERG HOSPITAL, STELLENBOSCH UNIVERSITY (SU)
THE DIVISION OF MEDICAL VIROLOGY AT NHLS GROOTE SCHUUR HOSPITAL, UNIVERSITY OF CAPE TOWN (UCT)

THE DIVISION OF MEDICAL VIROLOGY AT NHLS GROOTE SCHUUR HOSPITAL, UNIVERSITY OF CAPE TOWN (UCT)

The Division of Medical Virology is supported by UCT and the NHLS. It contributes to the diagnosis, treatment, prevention and eradication of viral diseases in South Africa through a diagnostic laboratory service together with a dynamic research and teaching programme. The NHLS virology diagnostic laboratory provides a comprehensive service to Groote Schuur Hospital and Red Cross Children's Hospital, and is one of two referral laboratories for the province. It offers a wide repertoire of tests in the fields of viral serology and molecular diagnostics. The laboratory has a special interest in molecular diagnosis of human viral diseases and performs an extensive range of viruses sequencing on site using Illumina sequencers.

UCT Team

The Division has a dynamic research, clinical and genomic teams that are closely connected with the NHLS laboratory on Groote Schuur Hospital.

UCT Investigators

- Prof. Carolyn Willianson
- Prof. Marvin Hsiao
- Assoc. Prof. Diana Hardie
- Dr Stephen Korsman

THE DIVISION OF VIROLOGY AT NHLS UNIVERSITAS ACADEMIC LABORATORIES, UNIVERSITY OF THE FREE STATE (UFS)

The laboratory is SANAS accredited under ISO15189 and serves as the referral diagnostic laboratory for NHLS laboratories in the Free State and Northern Cape provinces, including diagnostic testing for SARS-CoV-2. Diagnostics facilities include serological and molecular testing, processing over 500 000 tests per year. The Division is also involved in research and training, with an active postgraduate programme, including 14 masters and doctoral students and three postdoctoral researchers. The University of the Free State - Next Generation Sequencing (UFS-NGS) Unit is an interdisciplinary genomics business and academic facility. The UFS-NGS Unit has undertaken several projects, including viral metagenomics, the African Enteric Viruses Genome Initiative, the WHO rotavirus surveillance study for Africa and targeted 16S and ITS metagenomics projects.

Free State Team

Permanent staffing includes three pathologists, four medical scientists, three registrars and 16 technical staff. Genomic data generation is produced on site by the UFS-NGS.

Free State Investigators

- Prof. Dominique Goedhals
- Mr. Armand Bester
- Dr Martin Nyaga
- Prof Felicity Burt

THE DIVISION OF VIROLOGY AT NHLS UNIVERSITAS ACADEMIC LABORATORIES, UNIVERSITY OF THE FREE STATE (UFS)
THE DIVISION OF VIROLOGY AT NHLS INKOSI ALBERT LUTHULI CENTRAL HOSPITAL (IALCH), UNIVERSITY OF KWAZULU-NATAL (UKZN)

THE DIVISION OF VIROLOGY AT NHLS INKOSI ALBERT LUTHULI CENTRAL HOSPITAL (IALCH), UNIVERSITY OF KWAZULU-NATAL (UKZN)

The laboratory is SANAS accredited under ISO15189 and serves as the referral diagnostic laboratory for NHLS laboratories in (KwaZulu-Natal (KZN), including diagnostic testing for SARS-CoV-2. Diagnostics facilities include serological and molecular testing, processing over one million tests per year. The division has a large Sanger sequencer (ABI 3730), which is normally used to produce viral genomic data. However, as part of this project the division of virology will collaborate with the KZN Research Innovation and Sequencing Platform (KRISP) of UKZN so data can be produced locally in Durban. Students completing the MBChB programme or relevant qualifications in the Health Sciences at UKZN have an invaluable opportunity to train as Virologists under a joint UKZN and NHLS Department.

NHLS IALCH and UKZN Team

Permanent staffing includes pathologists, medical scientists, registrars and technical staff.

NHLS IALCH and UKZN Investigators

- Dr. Nokukhanya Mdlalose
- Dr. Pravi Moodley
- Prof. Koleka Mlisana

NATIONAL INSTITUTE FOR COMMUNICABLE DISEASES (NICD)

The NICD laboratory is a national and global SARS-CoV-2 reference laboratory. It has supported the establishment of laboratory protocols to SARS-CoV-2 in several African countries. NICD has also provided technical support and inter-laboratory comparison material for those laboratories. It has been a recognized World Health Organization (WHO) National Influenza Centre since the late 1980’s and is accredited by SANAS for ISO15189 as a medical testing laboratory. The Centre for Respiratory Diseases and Meningitis (CRDM) operates a BSL2 facility consisting of an RNA extraction, virus isolation and molecular laboratory with separate pre- and post-PCR settings as well as a BSL3 laboratory. NICD has also a genomics core that has illumina, PacBio, ONT and ABI Sanger sequencers.

NICD Team

The laboratory consists of 15 full time and contract employees. It is supported by the NICD sequencing core.

NICD Investigators

- Prof. Jinal Bhiman
- Dr. Arshad Ismai
- Dr. Mushal Ali

NATIONAL INSTITUTE FOR COMMUNICABLE DISEASES (NICD)
KRISP: KZN Research Innovation & Sequencing Platoform, University of KwaZulu-Natal

KRISP: KZN Research Innovation & Sequencing Platoform, University of KwaZulu-Natal

KRISP’s genomics laboratory will support the sequencing of samples from KZN. KRISP supports four sequencing platforms (i.e. Illumina, Oxford Nanopore Technologies, Sanger and S5 Ion). KRISP will also provide bioinformatics infrastructure for the consortium with bioinformatic servers and applications needed for the analysis of high-throughput genomic sequences produced by both KRISP and other genomics laboratories. In addition, KRISP will also manage the consortium and provide training to other laboratories and groups in the production and analysis of genomic data in South Africa.

KRISP Team

KRISP has a multi-disciplinary team with clinicians, laboratory scientists and epidemiologists. KRISP’s team also includes software developers and bioinformaticians.

KRISP Investigators

Dr. Jennifer Giandhari – Dr. Eduan Wilkinson – Dr. Benjamin Chimukangara – Dr. Richard Lessells – Dr. Inbal Gazy – Dr. Maryam Fish – Dr. Lavanya Singh – Dr. Aquilah Kanzi - Khulekani Khanyile (MSc) - Sureshnee Pillay (MSc) - Houriiyah Tegally (MSc) - Vagner Fonseca (MSc) - San James (MSc) – Prof. Tulio de Oliveira

THE COMPUTATIONAL BIOLOGY DIVISION AT THE UNIVERSITY OF CAPE TOWN (UCT)

The Computational Biology (CBIO) division at the University of Cape Town is the centre of bioinformatics activities at the university. It forms part of the Department of Integrative Biomedical Sciences and is located within the Institute of Infectious Disease and Molecular Medicine, in the Faculty of Health Sciences. The division leads H3ABioNet, an NIH-funded Pan African bioinformatics network for H3Africa. Research in the division focuses on understanding the genetic underpinnings of viral and bacterial diseases, studying human genetic diversity and genetic factors underlying disease susceptibility, understanding how the human microbiome impacts immunity and disease, and the development of computational analysis tools.

Team

Comprises a well-integrated group of academics, postgraduate students and technical support staff which collaborate extensively with, and provide computational analysis support to, other research groups within the IDM

Investigators

- Prof. Nicola Mulder
- Assoc. Prof. Darren Martin

THE COMPUTATIONAL BIOLOGY DIVISION AT THE UNIVERSITY OF CAPE TOWN (UCT)
South African National Bioinformatics Institute (SANBI)

South African National Bioinformatics Institute (SANBI)

SANBI’s research and development portfolio includes pathogen genomics where a team of academics, postgrad students and technical staff are developing computational tools to support the analysis of high throughput pathogen sequencing data to inform a public health response. We host the secretariat for the Public Health Alliance for Genomic Epidemiology (PHA4GE) – a global alliance to coordinate the provision and development of data standards for public health bioinformatics.

Team

SANBI has a large team of bioinformaticians and programmers.

Investigators

- Professor Alan Christoffels
-Peter van Heusden

Center for Quantum Technology at University of KwaZulu-Natal

The Centre for Quantum Technology is a Research Group headed by Prof. Francesco Petruccione and is hosted within the School of Chemistry and Physics at the University of KwaZulu-Natal. This group also lead the Big Data Flagship program of UKZN that bring together physicists, mathematicians and computer scientists. They are devoting their time to real-time analysis of COVID-19 data in South Africa.

Team

Theoretical, experimental and computational physicians.

Investigators

- Prof. F. Petruccione
- Dr. I. Sinayskiy
- Dr. M. Schuld

Center for Quantum Technology at University of KwaZulu-Natal