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The Developing Excellence, Leadership and Training in Science in Africa (DELTAS Africa) programme, funds Africa-based scientists to amplify the development of world-class research and scientific leadership on the continent while strengthening African institutions. DELTAS Africa is implemented through the AESA Platform. AESA (Alliance for Accelerating Excellence in Science in Africa) is a funding, agenda-setting, programme management initiative of the African Academy of Sciences (AAS), the African Union Development Agency (AUDA-NEPAD), founding and funding global partners, and through a resolution of the summit of African Union Heads of Governments. DELTAS Africa is supported by Wellcome and the United Kingdom Foreign, Commonwealth and Development Office (FCDO formerly DFID). The ongoing DELTAS Africa is a USD 100 million programme, funding eleven consortia spanning 54 institutions from Africa and 24 European institutions.

DELTAS Africa’s 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 DELTAS Africa Theory of Change (TOC) 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 eleven DELTAS Africa funded consortia were able to leverage on the TOC 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 closer look at how IDeAL researchers are working with the KEMRI-Wellcome Trust Research Programme (KWTRP) to understand and combat COVID-19 in Kenya. From Polymerase Chain Reaction (PCR) testing and data collection to engaging the public with the science behind the pandemic, we explore the benefits of a multidisciplinary approach to tackling COVID-19.

COVID-19 in Kenya

COVID-19 first hit Kenya at the beginning of March 2020. Initially, the cases trickled in at a rate of 5–10 per day, but by June the trickle had turned into a deluge of hundreds of cases per day. As of the date of writing of this blog 18 Feb 2021), COVID-19 cases and deaths in the country have already tipped 103,000 and 1,800 respectively.

The first challenge for the country was the establishment of testing capacity. Unfortunately, most hospital diagnostic labs were not set up to conduct the complex COVID-19 PCR tests. It therefore behooved the better equipped research institutions to assume the responsibility.

KEMRI-Wellcome Trust Research Programme’s initial response to COVID-19

KWTRP, the host institution for IDeAL, has over the last 30 years made huge investments in infrastructure, human resource and management systems to support research on the major and emerging causes of morbidity and mortality in Africa. The Programme was therefore able to rapidly deploy its resources to support COVID-19 response in Kenya. KWTRP also took advantage of our multidisciplinary approach to maximise synergy across COVID-19 research and response support activities.

The Programme was the first to set up PCR testing for COVID-19 in Kenya and has remained at the forefront of testing to date, particularly in the coastal region. The testing team, led by Dr Isabella Oyier and Dr Charles Nyaigoti (an IDeAL Mid-Career Fellow), has carried out over 90,000 tests; roughly half of all the tests carried out in the coastal region so far. Importantly, to address the challenge of diminished supply of testing reagents, the team established a new protocol for pooled testing to economise the use of reagents and reduce testing turnaround time

Collecting data to understand COVID-19 transmission in Kenya

Beyond supporting testing, we sought to address the lack of data on disease spread at population level that was hampering the ability of the government to make evidence-based decisions on COVID-19 control measures. Limited resources meant that it was not possible to conduct mass-testing. Therefore, researchers at the Programme employed two alternative ways of determining the transmission patterns and rate in the country.

The first was the application of genomic sequencing to determine when the COVID-19 virus entered the country and how it was spreading across the population. Since March 2020, we have sequenced nearly 500 viral genomes and made a significant contribution to the African COVID-19 genome sequence database. This work, led by George Githinji (past IDeAL Early Career Research Fellow), revealed multiple lineages of the virus suggesting that COVID-19 entered Kenya at multiple instances. Furthermore, the work revealed the viruses circulating in the country were the same as those in Europe and elsewhere; which is good news for the deployment of vaccines developed in other parts of the world.

The second approach involved using a test to determine how many people have COVID-19 antibodies in their blood as a proxy for previous infection. Researchers at the Programme developed an ELISA kit for sero-surveillance (which remains to date the only locally developed assay run in sub-Saharan Africa participating in the WHO standardization scheme). By applying this test to samples acquired from blood banks in the country, Dr Sophie Uyoga (IDeAL Mid-Career fellow), concluded that the number of people who have had a COVID-19 infection in the past is well above the number reflected in the targeted testing of those with suggestive symptoms. We are now using our clinical research network of over 30 hospitals spread across the country to track the numbers of patients with COVID-19 like symptoms over time (even if not tested) so as to add to the results of the blood donors samples.

The data arising from the testing, sequencing and sero-surveillance work are being used by mathematical and geospatial modellers in the Programme (including several IDeAL PhD and postdoctoral fellows) to predict disease incidence in different parts of the country. An example of the output of the modelling is a map that was developed by Peter Macharia (recent IDeAL PhD graduate) which combines biological susceptibility factors and health system parameters to generate a combined vulnerability index for populations across different counties in Kenya.

A multidisciplinary approach to combatting COVID-19

Building on the multidisciplinary approach, our bioscience platform is also supporting COVID-19 immunology studies, some of which are riding on the ChAdOx1 nCoV-19 vaccine trial that commenced early late last year at the KWTRP (led by Dr Mainga, past IDeAL Early Career Research Fellow).

On the other hand, our health systems research team and health economics teams are using the data and output of the models to examine the health system preparedness and to determine the cost effectiveness of COVID-19 control measures. Several social science studies are embedded within the same framework including those looking at the challenges of research ethics reviews during pandemics and gender issues (Kelly Muraya, IDeAL Early Career Research fellow) in relation to the pandemic. This integrated approach has led to over 30 policy briefs and provided the Ministry of Health in Kenya with real-time projections of incidence, health care demand, cost-effectiveness of control measures, and health facilities preparedness for rapid decision making on the deployment of control measures.

Engaging the public

As we continue to support COVID-19 research and responses, we are acutely aware of the fears and anxieties that the pandemic has stirred among the general public. This has been exacerbated by a flood of fake news and conspiracy theories. In response, IDeAL, together with the KWTRP’s communications team, has adopted a multi-pronged strategy for engaging the public to educate and dispel fake new and rumours related to the disease.

Over the last 3 months, we have conducted an intensive engagement campaign using social media broadcasts, key social media influencers and radio shows to reach even the most marginalised populations. For example, currently we have a series of radio shows with Ghetto Radio that are aimed at young people in the slums of Nairobi and another series with Kaya FM reaching out to the rural and urban public at the Kenyan coast. Both radio shows provide a platform for conversations with different publics in the country regarding COVID-19 transmission, control measures, treatment and the upcoming vaccine trials.

Research opportunities amid a pandemic

As is the case elsewhere, the pandemic has been a major test for Kenya’s emergency preparedness and health system resilience. However, it has also afforded IDeAL and KWTRP the opportunity to demonstrate the value of long-term investment in research infrastructure, human resource and management, and the importance of an integrated multidisciplinary framework for health research.

This blog was authored by Professor Samson Kinyanjui, Director of the Initiative to Develop African Research Leaders (IDeAL) and Head of Training and Capacity Building at the KEMRI-Wellcome Trust Programme in Kenya.