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.
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.
The diagnostic team is well integrated with the research and clinical teams. They are supported by the genomics team, who produce data on site.
- Prof. Susan Engelbrecht
- Prof. Gert Van Zyl
- Prof. Wolfgang Preiser
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.
The Division has a dynamic research, clinical and genomic teams that are closely connected with the NHLS laboratory on Groote Schuur Hospital.
- Prof. Carolyn Willianson
- Prof. Marvin Hsiao
- Assoc. Prof. Diana Hardie
- Dr Stephen Korsman
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.
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.
- Prof. Dominique Goedhals
- Mr. Armand Bester
- Dr Martin Nyaga
- Prof Felicity Burt
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.
Permanent staffing includes pathologists, medical scientists, registrars and technical staff.
- Dr. Nokukhanya Mdlalose
- Dr. Pravi Moodley
- Prof. Koleka Mlisana
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.
The laboratory consists of 15 full time and contract employees. It is supported by the NICD sequencing core.
- Prof. Jinal Bhiman
- Dr. Arshad Ismai
- Dr. Mushal Ali
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 has a multi-disciplinary team with clinicians, laboratory scientists and epidemiologists. KRISP’s team also includes software developers and bioinformaticians.
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 (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.
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
- Prof. Nicola Mulder
- Assoc. Prof. Darren Martin
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.
SANBI has a large team of bioinformaticians and programmers.
- Professor Alan Christoffels
-Peter van Heusden
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.
Theoretical, experimental and computational physicians.
- Prof. F. Petruccione
- Dr. I. Sinayskiy
- Dr. M. Schuld
The Department Medical Virology is supported by NHLS-TAD and UP. The NHLS-TAD Virology lab is a SANAS accredited diagnostic laboratory under ISO15189 that serves the public sector hospitals and clinics (including Steve Biko Academic hospital) in the Tshwane municipality and other areas of Gauteng. The Department of Medical Virology also provides teaching and training to medical technologists, medical technicians, intern medical scientists as well as to postgraduate students. The department has several research teams including HIV and opportunistic infections, enteric and enviromental, pappilomavirus and hepatitis, Biosurveillance and ecology of emerging zoonoses (BEEZ) and the Zoonotic arbo and respiratory virus Research programs (ZARV). The NHLS laboratory and ZARV program closely collaborate with the Network for Genomic surveillance in South Africa on COVID-19. The ZARV program focuses on virological, serological, and molecular epidemiological investigations of emerging respiratory and vector borne viruses including COVID-19. The group culture SARS COV-2 and emerging zoonotic viruses in a state of the art BSL3 lab that is part of the Centre for Viral Zoonoses within the department. The ZARV group is responsible for NGS sequencing using an Iseq sequencer for rapid sequencing of genomes or larger scale Illumina sequencing in collaboration with KRISP and NICD. The COVID-19 genomic sequencing program is funded through the MRC genomic surveillance COVID-19 grant of KRISP as well as a collaboration grant with the Robert Koch institute from the GIZ and BMBF as part of the African Network for Improved diagnostics and epidemiology of common and emerging infectious agents (ANDEMIA) and the G7 Global Health fund.
The University of Pretoria and NHLS Tshwane team
- Prof Simnikiwe Mayaphi (HOD)
- Prof Marietjie Venter (Head: ZARV, UP)
- Dr Adriano Mendes (postdoctoral fellow)
- Dr Amy Strydom (postdoctoral fellow)
- Ms Michaela Davis (MSc)