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The Minister of Higher Education, Science and Innovation, Dr Blade Nzimande, announced that the Department of Science and Innovation, will fund the KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP) to the tune of R25 million (of the R45 million required) over the next 12 months to complete the sequencing of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) 10,000 genomes in South Africa and Africa.

Minister Nzimande made the announcement, on the 18th December 2020, during a joint Department of Science and Innovation and the Department of Health and Scientists media briefing. This was in the wake of the latest surveillance results that shows a worrying trend of the highly transmittable COVID -19 variant first identified in the Eastern Cape (Nelson Mandela Bay) and moved to the Western Cape, KwaZulu-Natal and is now the dominant (possibly the only) Covid-19 variant responsible for the current surge.

The funding will be used to understand the spread of COVID-19 and other virus lineages in the continent and to support the clinical and laboratory investigations of the genomic variation in the country.

“This is in line with the use of pathogen genomics for monitoring of transmission dynamics of infectious agents and potential vaccine escape is of crucial importance to South Africa, Africa and the world,” said Minister Nzimande.

Minister Nzimande said that these funds will be used to acquire equipment to automate the sequencing system and to buy the reagents and other laboratory consumables. 

Minister Nzimande further pointed out that “In April 2020, the Department of Science and Innovation (DSI) through the Strategic Health Innovation Partnership, funded KRISP for a project: ‘Spatial and Genomic monitoring of COVID-19 cases in South Africa in order to fight the flames before they become a wild fire’. The initial funding was for approximately R10 million.  This resulted in the establishment of the Network for Genomic Surveillance in South Africa (NGS-SA) in June 2020, with the goal to sequence the genome of at least 10,000 severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) samples to inform the public health response in South Africa and to use spatial and genomic monitoring of COVID-19 cases to help the government to identify hotspots of transmission and control the local epidemic.”

The Minister further said that a critical next step is to get a better understanding of whether there is any clinical and epidemiological evidence to suggest increased transmissibility and/or pathogenicity of the virus and/or vaccine escape.

“In order to expand the access of genomic methods in South Africa, KRISP distributed whole genome sequencing protocols for Illumina and Oxford Nanopore Technologies sequencers and build capacity at various universities. KRISP also quickly genotyped the first one hundred strains of SARS-CoV-2 that were detected in South Africa. This will allow them to understand the level of genetic diversity circulating in the country,” Minister Nzimande emphasised.

Minister Nzimande said that the Network for Genomics Surveillance in South Africa (NGS-SA), have produced 2,800 genomes, which are publicly available at GISAID (The global science initiative and primary source that provides open-access to genomic data of influenza viruses and the novel coronavirus responsible for COVID-19).

“This has informed an understanding of the introduction and early spread of SARS-CoV-2 in South Africa, and have identified a number of SARS-CoV-2 lineages that are unique to South Africa, said Minister Nzimande.

KRISP was established in 2017 and situated at the University of KwaZulu-Natal’s Nelson R. Mandela School of Medicine, and is a cutting-edge genomics Centre offering a range of DNA sequencing, precision medicine testing, bioinformatics services and technologies to academic, industrial and commercial users.

Minister Nzimande said KRISP as a platform of the Technology Innovation Agency (TIA) - an agency of the Department of Science and Innovation (DSI)- a flagship programme of the South African Medical Research Council has established a world-class scientific infrastructure.

“Their vision is to challenge the status quo and establish one of the worlds most advanced and respected genetic sequencing platforms, in order to enable and support world-class genomics research and diagnostics services in Africa,” added the Minister.

The consortium capacitated five key National Health Laboratory Services (NHLS) and their associated academic institutions to produce and analyse whole viral genomes in South Africa in near real-time.

The main investigators are: 

Prof. Tulio de Oliveira (KRISP/UKZN)
Prof. Carolyn Willianson (University of Cape Town/ NHLS)
Dr. Jinal Bhiman (NICD)
Dr. Nokukhanya Msomi (UKZN/NHLS)
Professor Diana Hardie (University of Cape Town/ NHLS)
Dr Marvin Hsiao (University of Cape Town/ NHLS)
Prof. Dr. Nicky Goedhals (University of the Freestate / NHLS
Prof. Susan Engelbrecht (Stellenbosch University / NHLS)

The three main objectives of the “Spatial and Genomic monitoring of COVID-19 cases in South Africa in order to fight the flames before they become a wild fire” study are:

To increase access to genomic methods in order to sequence SARS-CoV-2 close to the source of outbreaks in South Africa.
To support the production and analysis of SARS-CoV-2 genomic data in South Africa in near real-time
To trace SARS-COV-2 introductions, identify community transmissions and use this information to characterize and control local outbreaks.

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Issued by:
Ministry of Higher Education, Science and Innovation
DST Building (53), CSIR Campus
Meiring Naude Road
Brummeria
Pretoria
Enquiries: Ishmael Mnisi 0660378859