AAS Open Research

How a South African-led research network is combatting COVID-19

COVID-19 in South Africa

The Developing Excellence, Leadership and Training in Science in Africa (DELTAS Africa) programme funds collaborative networks/consortia led by Africa-based scientists to amplify Africa-led development of world-class research and scientific leaders on the continent, while strengthening African institutions. The ongoing DELTAS Africa I is a USD 100 million programme funding 11 programmes spanning 54 institutions from Africa and 24 European institutions.

DELTAS Africa’s ultimate goal is to produce researchers with the capacity to publish and lead locally relevant and high-quality research to impact health science, policy and practice in Africa. To achieve this the Theory of Change (TOC) for DELTAS is predicated on building research leadership through supporting growth of excellent research environments, scientific citizenship, research training and scientific quality.

This blog series explores how the 11 DELTAS funded consortia were able to leverage on the TOC for DELTAS and pivot in real time to support an Africa-wide response to COVID-19, influencing research and policy across the continent and beyond.

In this blog post, we take a look at how researchers and institutions supported by the South African based Sub-Saharan Africa Consortium for Advanced Biostatistics training (SSACAB) moved fast to conduct essential COVID-related research.

Supporting regional and national government response in South Africa

Members of the SSACAB consortium have been very active in carrying out research to support both national and provincial government in South Africa in the fight against COVID-19. South Africa has been the African country hardest hit by COVID-19, in regard to both infection rates and deaths. As of December 2020, the continent had so far recorded 49,961 deaths of which South Africa contributed approximately 42% of all COVID-19 deaths in Africa

As the pandemic took hold in South Africa, the minister of Health set up advisory committees made up of experts from different disciplines. Provincial coordinating committees were also set up to receive on-the-ground information from research teams and other arms of COVID-19 response teams. SSACAB members played a central role in many of these teams.

The Gauteng province established a “War Room”, where different teams would come together to report on relevant evidence. The research and modelling team included SSACAB colleagues from the Division of Epidemiology & Biostatistics at Witwatersrand, who joined other experts from local universities and research institutions including the South Africa Medical Research Council (SA MRC).

SSACAB consortium member, Dr Innocent Maposa, was part of a team that assessed and reviewed evidence on possible implications of the pandemic outbreak on frontline healthcare workers by conducting a rapid scoping review. As a result of sharing findings with the “War Room” Provincial Coordinating Committee, research on the mental health of healthcare workers was instituted to assess the impact of the pandemic on healthcare workers in the province.

Additionally, Dr Maposa and Professor Eustasius Musenge are working on a project with the Gauteng Department of Health on the impact of COVID-19 on Health Systems Performance, focusing on the priority health programmes of Gauteng Health. Dr Maposa is also involved in the population-based sero-epidemiological investigation (whereby specific markers in blood serum are measured to establish incidence and distribution of the disease) of SARS-COV-2 virus infection in Gauteng province, which seeks to ascertain the levels of infection through antibody testing.  

Impact of underlying health conditions on COVID-19 disease progression

Also at Stellenbosch University, in the Western Cape, South Africa, Professor Birhanu Teshome Ayele and his collaborators at Tygerberg Hospital carried out a systematic review of evidence on the implications of COVID-19 in high HIV/TB burdened countries. They note that TB was a risk factor for COVID-19, both in terms of severity and mortality, irrespective of HIV status. They suggest structured diagnostic algorithms and clinical management of COVID-19/HIV/TB or COVID-19/TB patients to improve co-infection outcomes.

Professor Ayele is further involved in COVID-19 studies including: a multicentre prospective cohort study of HIV and SARS-CoV-2 co-infected hospitalized adults in Cape Town; effectiveness of corticosteroids among patients with severe COVID-19 at Tygerberg Intensive Care Unit; and the blood? and related laboratory findings in adult patients with confirmed COVID-19. The team published a methodology research protocol with British Medical Journal (BMJ) Open and anticipate more scholarly work to follow.

Professor Samuel Manda worked with the National Department of Health and other scientists from the SA MRC to provide evidence critical to managing comorbidities among COVID-19 patients, whereby multiple diseases or health conditions may also be affecting the same patient at the same time as COVID-19. The study identified individuals at high risk, including the elderly and those with comorbidities (hypertension and diabetes mainly), recommending that careful attention should be given to these individuals during the COVID-19 pandemic period across the country.

Professors Manda and Henry Mwambi, with other local scientists from the Council for Scientific and Industrial Research (CSIR) and the Human Sciences Research Council (HSRC), contributed to a novel data-driven, real-time statistical model for estimation and prediction of COVID-19 cases and deaths in South Africa. By employing the use of previously validated models and comparing the results to the real-time observed values over forecasting periods of 5–30 days, the team concluded that their model could be applied to reliably predict deaths and cases over periods of 5–10 days, but that forecasts for longer periods underestimated cases. The group further recommends the application of their model to daily cumulative COVID-19 cases and deaths data to guide or reinforce the need for social distancing, as well as personal protective measures such as regular hand washing and the wearing of PPE.

SSACAB uses AI and data science in pandemic responses and conducts first COVID-19 trials in South Africa and Kenya

Dr Sylvia Muyingo of the African Population Health Research Centre (APHRC), and the Implementation Network for Sharing Population information from Research Entities (INSPIRE) team – including Professor Jim Todd – obtained a grant from the International Development Research Centre (IDRC-Canada) to build a database for COVID-19 data in Kenya and Malawi.  The grant harnesses heterogeneous COVID-19 data using artificial intelligence and data science to build a data hub and support analysis for public health decision making in the two countries. The initial data will follow the format of the Wellcome Trust LMIC COVID-19 questionnaire for population data (Austin et al, 2020) and the World Health Organization (WHO) COVID-19 case report forms (CRF) for clinical data (ISARIC, 2020). The project will develop accurate, real-time programs to produce FAIR (findable, accessible, interoperable, reusable) data with methodological rigor to plug the gaps in data needed at the national level, and to assist international efforts to make informed decisions about the spread of COVID-19 in Africa.

In Kenya, Benedict Orindi is presently working with the team at the Kenya Medical Research Institute (KEMRI)-Wellcome Trust Research Programme in Kilifi on a Phase Ib/II COVID-19 vaccine trials of the ChAdOx1 nCoV-19, developed by the University of Oxford in partnership with the pharmaceutical company AstraZeneca. The trials will determine the safety and effectiveness of the vaccine in Kenyan adults over the age of 18 years, initially involving 40 frontline healthcare workers in Kilifi County. A further 360 volunteers will be recruited once the vaccine is deemed safe in the initial population, with potential for expanding the trials into Mombasa County. Kenya and South Africa are the only African countries participating in the trial.