The NRF's Contribution to the Global Covid-19 Challenge

COVID-19 AFRICA RAPID GRANT FUND 

A COVID-19 Africa Rapid Fund Grant with an initial total funding of approximately USD4.75million, close to R90 million, has been launched to address research questions and implement science engagement activities associated with the pandemic. 

The National Research Foundation (NRF) supported by South Africa’s Department of Science and Innovation (DSI), Canada’s International Development Research Centre (IDRC), the Fonds de Recherche du Québec (FRQ), the Swedish International Development Cooperation Agency (Sida), the United Kingdom’s Department for International Development (DFID), United Kingdom Research and Innovation  (UKRI) through the Newton Fund, and SGCI participating councils are collaborating in this initiative, which has been conceptualised under the auspices of the Science Granting Councils Initiative in Sub-Saharan Africa (SGCI).

The Fund aims to support knowledge generation and translation to inform diagnostics, prevention and treatment of COVID-19, strengthen African regional and continental science engagement efforts in response to the pandemic, and leverage existing multilateral collaborations and attract new collaborations from international partners.

The COVID-19 Africa Rapid Fund Grant Fund will support projects in three areas: 1) research; 2) science engagement – call to science and health journalists and communicators; and 3) science engagement – call to science advisers in response to the global COVID-19 pandemic.

COVID-19: Research efforts by DSI-NRF CoE’s and SARChI Chairs

DSI- NRF CENTRE OF EXCELLENCE IN MATHEMATICS AND STATISTICS SCIENCES (COE MASS)

The CoE Mass sits across 16 Nodes located at Universities and Sciences Councils with its Admin Hub located at Wits University. During the current COVID-19 global pandemic, CoE-MaSS researchers are working on the following research:

• Prof Melusi Khumalo (Department of Mathematical Sciences, University of South Africa) and his international collaborator Prof Talat Nazir (Pakistan) are looking at ways to classify and separate infected and non-infected people as COVID-19 spreads rapidly throughout society. They are using a machine learning tools, more specifically the support vector machine (SVM) method, to see whether this method will be able to detect COVID-19 in patients, using X-ray images and statistics. Training a SVM (classification, regression and novelty detection) requires the solution of a very large quadratic programming problem, which the team is reviewing. They want to understand better whether the SVM method will be able to be used to detect COVID-19 in patients.
   
• Prof Andriette Bekker (Department of Statistics, University of Pretoria) along with international collaborators from the University of Neyshabur and also the Shahrood University of Technology, both in Iran, have developed an interactive app using R shiny application which provides a synergetic web-based dashboard from COVID-19 data to track COVID-19 demographic information.
   
• Dr Johan Ferreira (Department of Statistics, University of Pretoria) is investigating the stochastic behaviour of incubation periods of viral respiratory diseases.
   
• Dr Salisu Garba and Prof Jean Lubuma (Department of Mathematics and Applied Mathematics, University of Pretoria) are working with international collaborator Prof Berge Tsanou (Cameroon) to propose a new mathematical model for the transmission dynamics of COVID-19. The model is used to assess the most effective measure in controlling the disease in the South African context. By fitting the daily incidence, the model is used to estimate the future trajectories. A manuscript is under preparation. The researchers are also further assessing the impact of non-pharmaceutical interventions such as social distancing, quarantine and isolation using the threshold quantities.
   
• Dr Faraimunashe Chirove (Department of Mathematics and Applied Mathematics, University of Johannesburg) is collaborating with Prof Farai Nyabadza, Dr Maria Vivien Viyasa and postgraduate students (all from UJ) on fitting current COVID-19 data to the designed mathematical models in the South African context, to predict future trends on the virus.
   
• Prof Farai Nyabadza (Department of Mathematics and Applied Mathematics, University of Johannesburg) is also working with international collaborators and using a mathematical model to fit the observed COVID-19 data in South Africa. The team used the fitted basic reproduction number to estimate the critical vaccination coverage required to control the disease under different hypothetical vaccine efficacy scenarios. They also estimated the percentage reduction in effective contacts due to social distancing measures implemented. The researchers have made several recommendations and these are summarized in a manuscript that has already been submitted for journal publication.
   
• Prof Henry Mwambi (School of Mathematics, Statistics and Computer Science, University of KwaZulu Natal) is part of a team linked to Council for Scientific and Industrial Research (CSIR) whose research is to develop data driven growth models for COVID-19 cases and other related outcomes.
   
• Prof Rao Appadu (Department of Mathematics and Applied Mathematics, Nelson Mandela University) and collaborating researchers (Dr Abey Kelil and PhD student, Mr Yusuf Tijani) are looking into using polynomial interpolation to predict COVID-19 propagation. In this work, the team makes use of four mathematical interpolation methods (three variations of Lagrangian interpolation, and Spline interpolation) to construct polynomials to capture the data for COVID-19 disease propagation. The team is looking at data on the total number of people infected and the number of active cases. This study looks at data from: Italy, Germany, South Korea, India, South Africa and Mauritius.

DSI-NRF SARChI CHAIR IN MATHEMATICAL AND THEORETICAL PHYSICS BIOSCIENCES

Prof Cang Hui (Department of Mathematics at Stellenbosch University) is collaborating with Chinese collaborators to develop an ecological model that captures the transmission pattern of the COVID-19 outbreak and a preprint was submitted on medRχiv in February 2020. In addition, this team has also carried out research investigating the successful containment of COVID-19. A preprint of this research was uploaded to medRχiv in March 2020.

DSI-NRF SARChI CHAIR IN MATHEMATICAL MODELS AND METHODS IN BIOSCIENCES AND BIOENGINEERING (M3B2)

Prof Jacek Banasiak (Department of Mathematics and Applied Mathematics at the University of Pretoria) is collaborating with colleagues (Prof Roumen Anguelov, Prof Jean Lubuma, and Prof Rachid Ouifki) on various research projects involving mathematical modelling of biological processes relating to COVID-19. The outputs of this research will be shared in the form of Technical Reports and journal publications. 

DSI-NRF SARChI CHAIR IN QUANTUM INFORMATION PROCESSING & COMMUNICATION 

Prof Francesco Petruccioneto (Pro-Vice Chancellor of Big Data Analysis at University of KwaZulu Natal) has partnered with KwaZulu-Natal Research and Innovation Sequencing Platform (KRISP) to put together a team with more than 20 researchers, including computer scientists, mathematicians, statisticians, bioinformaticians, infectious diseases clinicians, theoretical physicists and quantum computing scientists to analyse the COVID-19 outbreak in South Africa.

To date, graphs produced by the team showing that South Africa is flattening the curve were used in the presentation by the Minister of Health and Prof Salim Abdool Karim, Chair of the COVID-19 Ministerial Advisory Committee to the nation on 13 April 2020.

SARAO MANDATED TO MANAGE THE NATIONAL RESPIRATORY VENTILATOR PROJECT

The South African Radio Astronomy Observatory (SARAO), a NRF managed National Research Facility, has been mandated by the he Department of Trade, Industry and Competition to manage the national effort to locally design, develop, produce and procure respiratory ventilators to support the government’s efforts to combat the COVID-19 pandemic. SARAO has been chosen based on the experience it gained in the development of complex systems for the MeerKAT radio telescope, a precursor to the world’s largest Square Kilometre Array radio telescope.

The South African Astronomical Observatory (SAAO), another NRF managed National Research Facility is supporting the SARAO coordinated ventilator effort by producing parts for ventilator prototypes.

DSI-NRF CoE’s and SARChI involvement

CAPRISA

• CAPRISA – including the DSI- NRF CoE in HIV Prevention – and the KwaZulu-Natal Research and Innovation Sequencing Platform (KRISP) is conducting a prospective epidemiological and phylogenetic study to establish how the SARS-COV-2 coronavirus is spreading in urban and rural KwaZulu-Natal in order to guide locally-appropriate prevention and clinical care.

The study aims to determine COVID-19 transmission in an urban and rural setting; understanding the impact of HIV and/TB co-morbidity on severity of COVID-19 presentation and outcomes; and advancing understanding of immune responses to COVID-19.

The study is funded by the Department of Science and Innovation (DSI) through South African Medical Research Council (SAMRC).

• The Director of the CoE in HIV Prevention, Professor Salim Abdool Karim and Quarraisha Abdool Karim are both members of the COVID-19 Ministerial Advisory Committee that is providing high level strategic advice to the Minister of Health and to support the National Department of Health in the response to the COVID-19 outbreak in South Africa.

Prof Salim Abdool Karim is the chair of the Ministerial Advisory Committee.

Professor Quarraisha Abdool Karim is a member of the Public Health Group on the Ministerial Advisory Committee and is also a Member of the Executive Group of the International Steering Committee for the COVID-19 SOLIDARITY Trial.

• Drs Nesri Padayatchi and Kogieleum Naidoo both from CAPRISA are leading the KZN Provincial Department of Health (DOH) response to COVID-19.

DSI- NRF COE IN EPIDEMIOLOGICAL MODELLING AND ANALYSIS (SACEMA)

The DSI- NRF CoE in epidemiological modelling and analysis (SACEMA) is a member of the national COVID modeling consortium and have mainly been working to provide short-term projections of case numbers.

The modelling work on COVID 19 is being coordinated through the National Institute of Communicable Diseases (NICD) and the National Department of Health (NDOH).

THE NRF COORDINATES A NETWORKING OF EXPERTS TO SUPPORT GOVERNMENT DEPARTMENTS

The NRF is coordinating a network of experts (Centres of Excellence and Research Chairs) across various universities to support the South African Government Technical Advisory Centre (GTAC). The NRF-GTAC initiative supports Government departments with rapid information, data and analysis through expert groups in Health, Immunology, Microbiological and related fields, including Sociology, Psychology, Data and Information, Economics, Systems Analysis and Food and Nutrition Science.

SAEON DATA CONTRIBUTES IN SHAPING SOUTH AFRICA’S RESPONSE TO COVID-19

The NRF’s South African Environmental Observation Network (SAEON), is the lead agency and implementer of the South African Risk and Vulnerability Atlas (SARVA). As part of this initiative by the Department of Science and Innovation (DSI), the SAEON team has been collecting, curating and analysing data relevant to understanding the risk and vulnerability of South Africa to a range of hazards. With the announcement of the spread of COVID-19 in South Africa, the team started creating a list of indicator data sets relevant to COVID-19.

The added value components SAEON has produced include:

1. A set of indicator dashboards indicating South Africa’s healthcare infrastructure; the potential high risk areas for spread of COVID-19; and vulnerability of people with a specific focus on age distribution and the burden of disease.
2. A customised version of the SARVA risk profiler COVID-19 that allows users to change the thresholds of risk such as changing the minimum number of beds required or the number of medical professionals to cope with the current rate of infection. This is to accommodate different regions across the country that may face context specific challenges.
3. Infographics to assist translating data as well as the risk and vulnerability indicators for decision-makers, e.g. hospital beds are used to indicate the availability of inpatient services. South Africa has on average 18 hospital beds per 10,000 uninsured population compared to Italy which has 34 beds per 10,000 population.

This data has been shared with COVID-19-focused teams such as the Council for Scientific and Industrial Research (CSIR) Task Team as well as the Telkom/National Institute for Communicable Diseases team.

iTHEMBA LABS IN A COLLABORATION THAT  PROVIDES AN ANALYTICS AND MONITORING TOOL FOR THE SPREAD AND IMPACT OF THE CORONAVIRUS IN SOUTH AFRICA

An interdisciplinary team of scientists from the University of the Witwatersrand and iThemba LABS, an NRF Research Facility that is the largest facility for particle and nuclear research in Africa, has collaborated with the data analytics team of Switzerland-based company, Data Convergence, to create a COVID-19 monitoring tool. The tool, called the COVID-19 South Africa dashboard, is being used to observe the development of the Coronavirus in South Africa. The tool uses data in conjunction with global inputs and local parameters to provide predictions for the spread and impact of the coronavirus in the country. Data is broken down into provincial, gender, age and transmission route, as well as an overview of Coronavirus in Africa and global trends.

The dashboard is aimed at informing government, scientists, the media and general public with quick, easy-to-understand information on the current situation.

Since the launch in 22 March 2020, the dashboard has grown with new data features, including snapshot views of how the pandemic is spreading in Africa, as well as statistics showing world trends, being added.

SAASTA  SUPPORTS 26 SCIENCE JOURNALIST INTERNS IN THEIR COVERAGE OF COVID-19

South African Agency for Science and Technology Advancement(SAASTA) a business unit of the NRF, is currently working with the South Africa Science Journalists’ Association to support 26 science journalist interns in their coverage of the COVID-19 pandemic in various SouthAfrican languages. The aim is to make scientific information accessible to all South Africans. In addition, the SAASTA team has developed a comprehensive database of contact details for scientists working within the health and virology research areas so that interns can contact credible experts for interviews. They have also created a dedicated social media group as a platform to share scientific information about the COVID-19 virus and latest media releases from the South African Government to assist interns in their coverage. SAASTA is also engaging with past interns from the Youth Science and Technology Journalism Programme.

SAIAB DONATES 1 250 LITRES OF ETHONOL FOR THE PRODUCTION OF HAND SANITISERS

The South African Institute for Aquatic Biodiversity (SAIAB) donated 1 250 litres of ethnol to Rhodes University in support of the University’s hand sanitiser manufacturing initiative. The initiative comes in the wake of sanitiser shortages.

DSI-NRF CENTRE OF EXCELLENCE IN BIOMEDICAL TB RESEARCH RESPONDS TO COVID -19

Drawing from the scientific expertise and experience in infectious diseases from a clinical and laboratory perspective, the DSI- NRF Centre of Excellence in Biomedical TB Research (CBTBR), is supporting Government’s interventions to tackle the COVID-19 pandemic in South Africa.

The CBTBR is, among other things, providing the National Health Laboratory Services (NHLS) and other stakeholders with control material to ensure that all Covid-19 tests are carried out in a quality assured manner and to evaluate the performance of new kits.  It has also played a key role in sourcing health and safety guidelines for enabling Biosafety Level 3 labs that are used primarily for TB research to be repurposed for work involving infectious materials from COVID-19 patients.  These guidelines have been sourced by drawing on the CBTBR’s wide network of international collaborators.