The recent outbreak of the new and highly transmittable Covid-19 variant has compelled the minister of higher education, science and innovation, Dr. Blade Nzimande, to fund the KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP) to the tune of R25 million – this is part of the R45 million required.
The announcement was made during a joint media briefing between the department of science and innovation (DSI) and the department of health and scientists.
South Africa is currently experiencing a new surge of Covid 19 transmissions which forced President Cyril Ramaphosa to announce new restrictions in provinces that have recorded spikes attributed to the new strain of Covid-19.
The funding will be over 12 months to complete the sequencing of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) 10,000 genomes in South Africa and Africa. The first province to experience a surge of the virus was the Eastern Cape, followed by the Western Cape, KwaZulu-Natal and it seems to be hitting Gauteng province.
KRISP was established in 2017 and situated at the University of KwaZulu-Natal’s Nelson R. Mandela School of Medicine. It 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.
According to minister Nzimande, 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.
Said minister Nzimande: “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.”
He said these funds will be used to acquire equipment to automate the sequencing system and to buy the reagents and other laboratory consumables. He further pointed out that in April 2020 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 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.
The initial funding was for approximately R10 million and it resulted in the establishment of the Network for Genomic Surveillance in South Africa (NGS-SA) in June 2020. The aim of the network is 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.
It will also use spatial and genomic monitoring of Covid-19 cases to help the government to identify hotspots of transmission and control the local epidemic, said minister Nzimande.
In addition, he said, a next critical 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,” said the minister. He added that KRISP also quickly genotyped the first one hundred strains of SARS-CoV-2 detected in South Africa. This will allow them to understand the level of genetic diversity circulating in the country.
He said NGS-SA have produced 2,800 genomes, which are publicly available at GISAID. This is 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.
The minister said KRISP as a platform of the Technology Innovation Agency (TIA) – an agency of the DSI- and a flagship programme of the South African Medical Research Council, has established a world-class scientific infrastructure.
Added minister Nzimande: “Their vision is to challenge the status quo and establish one of the world’s most advanced and respected genetic sequencing platforms, in order to enable and support world-class genomics research and diagnostics services in Africa.”
The consortium capacitated five key National Health Laboratory Services (NHLS) and their associated academic institutions, he said, to produce and analyse whole viral genomes in South Africa in near real-time.
The main investigators involved in the initiative are:
1. Professor Tulio de Oliveira (KRISP/UKZN)
2. Professor Carolyn Willianson (University of Cape Town/ NHLS)
3. Dr. Jinal Bhiman (NICD)
4. Dr. Nokukhanya Msomi (UKZN/NHLS)
5. Professor Diana Hardie (University of Cape Town/ NHLS)
6. Dr Marvin Hsiao (University of Cape Town/ NHLS)
7. Dr.Nicky Goedhals (University of the Free State / NHLS
8. Professor Susan Engelbrecht (Stellenbosch University / NHLS)