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African data science research receives major funding from the National Institutes of Health, USA

Several members of the Human Heredity and Health in Africa (H3Africa) Consortium are among the beneficiaries of a $74.5 million investment from the National Institutes of Health (NIH) to develop data science, innovation, and health discoveries across Africa. They are among the recipients of 19 awards under the NIH’s new Harnessing Data Science for Health Discovery and Innovation in Africa (DS-I Africa) program to support research, ethics, and training activities.

The NIH forms part of the USA’s Department of Health and Human Services and is the main federal medical research agency that conducts and supports basic, clinical, and translational medical research, and investigates the causes, treatments, and cures for both common and rare diseases. Over the past decade, the NIH, together with the Wellcome Trust, has funded H3Africa, enabling the Consortium to support ground-breaking research projects that have paved the way to developing solutions to improve health on the continent and globally.

Professor Alash’le Abimiku, director of the laboratory clinical services at the Institute of Human Virology in Nigeria (IHVN), a recipient of a DS-I research hub award for ‘INFORM Africa’ (Role of Data Streams in Informing Infection Dynamics in Africa), and who has been pivotal to the establishment of long-term collaborations between the IHVN and research institutes around the world says: “The award from DS-I Africa is significant as it presents an opportunity to consolidate on gains from other pan African consortiums led by African scientists such as H3Africa on health issues of significant public health challenge to the African continent. African scientists and public health leaders should benefit from the immense strength that comes from the current era of sharing big data freely and openly for insights to address health issues and outbreaks. Thus, for INFORM-Africa, scientists in Nigeria, South Africa, and Zambia came together to partner with colleagues at the University of Maryland USA to use big data from SARS CoV-2 and HIV syndemics with the overall goal to provide population-based information on transmission dynamics to inform interventions and as a cornerstone for future pandemic preparedness.”

The other projects within H3Africa receiving awards are:

The Computational Omics and Biomedical Informatics Program (COBIP)
For this Research Training Program, the University of Cape Town (UCT) is partnering with Oregon Health & Science University to provide interdisciplinary training opportunities to develop the next generation of researchers working on aspects of fundamental data science, computational omics, and imaging data science. COBIP will place a strong emphasis on training graduate students and faculty from participating African institutions, through a combination of contact and online teaching, research projects and internships, to foster biomedical data science research that will build critical capacity in data science and drive the development of innovative solutions to African health challenges.

Project lead: Emile Chimusa is an Associate Professor in the Division of Human Genetics in UCT’s Department of Pathology. Chimusa’s main research interests lie in developing statistical and machine learning methods for uncovering the genetic basis of human disease and the genetics underlying these methods.

Makerere University Data Science Research Training to Strengthen Evidence-based Health Innovation, Intervention and Policy (MakDARTA) – Uganda
Africa is facing a triple burden of disease which is a high incidence of fatal infectious diseases, non-communicable diseases, and emerging epidemics (with pandemic potential). Addressing these will require new thinking and approaches for generating and synthesizing evidence that can inform policy. Research training will provide an avenue to build capacity for locally generated investigations aimed at preventing and controlling these diseases. Leveraging on existing infrastructure at Makerere University College of Sciences and international collaboration with Johns Hopkins University, this project will develop a comprehensive multi-disciplinary data science research-training program in Uganda.

Project lead: David Kateete is a lecturer in the Department of Microbiology at Makerere University in Kampala, Uganda

The Combating AntiMicrobial Resistance in Africa Using Data Science (CAMRA) project will study antimicrobial resistance and the dynamics of disease transmission, develop a portable screening tool for bacterial infections, and test a potential antimicrobial compound. Bacterial infections are highly prevalent and contribute significantly to morbidity and mortality across all age groups, but because appropriate bacterial diagnostic services are nonexistent or very limited, finding the true cause of most infections and the true spread of antimicrobial resistance (AMR) is a major challenge in Africa, where data is limited.

Project lead: Christian Happi is a professor of molecular biology and genomics and the director of the African Center of Excellence for Genomics of Infectious Diseases (ACEGID) at Redeemer’s University in Nigeria. He researches the human genome as well as the genomics of infectious diseases, including malaria, Lassa fever, Ebola, yellow fever, monkeypox, coronavirus, and HIV. Happi used next generation sequencing technology to perform the first sequence of the SARS-CoV-2 virus in Africa within 48 hours of receiving the sample. This seminal work, which provided insight into the detailed genetic map of the coronavirus in Africa, confirmed the origin of the virus, and paved the way for the development of new countermeasures, including new diagnostics, therapeutics, and vaccines

The MADIVA Research Hub will study multi-disease morbidity by analyzing clinical and genomic data with the goal of providing actionable insights to reduce disease burden and improve overall health. Researchers will develop data science techniques and solutions to tackle the problem of multimorbidity in Africa – the problem of multiple co-occurring diseases that significantly add to the health burden in Africa. MADIVA will work primarily on research sites in rural Bushbuckridge, South Africa and urban Nairobi, Kenya and building on the significant resources of the SAMRC/Wits Agincourt Rural Public Health and Health Transitions Research Unit and the African Population & Health Research Centre (APHRC), Nairobi which have long track records in working in these communities. The core of the data to be analysed is from H3Africa-funded research.

Project lead: Professor Scott Hazelhurst is based at the Wits Health Consortium (University of the Witwatersrand, South Africa). The Co-PIs are Catherine Kyobutungi (APHRC), Michèle Ramsay and Stephen Tollman (Wits) with a focus on big data in genomics medicine.

The Public Understanding of Big data in Genomics Medicine in Africa (PUBGEM-Africa) based at UCT aims to use empirical methods to address some of the pertinent potential ethical, legal and social implications (ELSI) issues. This is particularly as it relates to models of public engagement in big data use for healthcare and innovation; identifying the equity-oriented roles and responsibilities of stakeholders involved in big data use for genomics person; understanding public attitude to and perceptions towards big data in genomics medicine and the governance of big data; the development of equity-oriented governance frameworks for big data use in genomics medicine; and the setting-up of an ELSI core that will host an ELSI help desk for data science in health in Africa and provide small grants and mentorship support to emerging data science bioethics scholars in Africa.

Project Lead: Ambroise Wonkam, based at the University of Cape Town, is a Professor of medical genetics and Director of GeneMAP (Genetic Medicine of African Populations). His research interests are reflected in more than 130 peer-reviewed publications. His research focuses on Sickle Cell Disease (SCD and Genetics of hearing loss in Africa. Wonkam is president of the African Society of Human Genetics and current chair of the steering committee of the H3Africa consortium, Board member of the International Federation of Human Genetics Societies, and steering committee’s member of the Global Genetic Medicine Collaborative (G2MC).

In addition, the University of Cape Town (UCT) will develop and manage the initiative’s eLwazi Open Data Science Platform (ODSP) and coordinating center to provide a central platform for the DS-I Africa researchers to enable them to access data,  tools and workflows, and run analyses through collaborative workspaces. This will be led by a well-established partnership between Prof Nicky Mulder (current PI H3ABionet) and Dr Michelle Skelton (current PI/Project Manager H3Africa Coordinating Centre). Leveraging on her experience of leading H3ABionet, a pan African Bioinformatics consortium aimed at data and informatics resource and capacity development, Mulder will establish the eLwazi platform, while Skelton will use her experience in coordinating the H3Africa consortium to develop an efficient coordinating centre (CC) which will address all the joint administrative, collaborative, and logistical needs of the DS-I consortium.