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Case study: How TIBA works together across Africa to tackle COVID-19 and other infections through rapid genomic sequencing

Scientists supported by the NIHR Global Health Research Unit on Tackling Infections to Benefit Africa (TIBA) partnership in four African countries have co-authored a landmark paper on the COVID-19 pandemic in Africa, published this month in the prestigious journal Science. The paper, entitled A year of genomic surveillance reveals how the SARS-CoV-2 pandemic unfolded in Africa is remarkable because it was the first such multi-country, and multi-centre study in Africa, and demonstrates the strength of African scientists working together.   It is also notable that Science, one of the world’s ‘top three’ journals, has published a paper co-authored by 303 African researchers! I am honoured to be one of these authors, and to have worked alongside some amazing colleagues during a very challenging year for all of us. This study highlights what can be achieved through collaboration across the continent.

TIBA - a brief history

TIBA, which means “to cure an infection” in Swahili, started in 2017 as one of the first NIHR-funded Global Health Research Units. Coordinated by Profs Mark Woolhouse and Francisca Mutapi at the University of Edinburgh, TIBA was designed to be an Africa-led partnership including multi-disciplinary researchers from 9 countries: Botswana, Ghana, Kenya, Rwanda, South Africa, Sudan, Tanzania, Uganda and Zimbabwe.

Our mission was not only to conduct excellent research in infectious tropical diseases, but also to empower African scientists to improve preparedness for epidemics in an effective and sustainable way. Although we had no idea of what was to come, epidemic preparedness was a key element of our work from the outset, and we developed a strategy to build the expertise and tools for real-time viral genomic sequencing capacity across Africa.

In December 2018, TIBA partnered with the ARTIC Network to run a practical course in Ghana to train researchers from 13 African countries in real-time virus genome sequencing using the Oxford Nanopore MinION sequencing portable platform. We then commissioned two projects to deploy the sequencing technology, working on rotavirus and measles epidemics in Botswana and Rwanda respectively.

COVID - a new challenge

By early 2020, all was going well with the work, and the results were extremely promising, and then COVID-19 struck! We knew that it was no longer ‘business as usual’ and we would need to respond to this new challenge. Throughout the pandemic, TIBA researchers in Africa applied the sequencing technology we had so recently introduced to support national efforts in generating SARS-CoV-2 genomes to inform the response. 

To date, four TIBA partner institutions in Southern (Botswana), West (Ghana) and East Africa (Kenya and Rwanda) have generated more than 5,000 SARS-COV-2 genome sequences representing about 15% of the genome sequencing data from the continent. In line with our open access policy, these sequences have been uploaded to the open access platform GISAID (Global Initiative on Sharing Avian Influenza Data) for the benefit of the wider global research network. 

These data from TIBA partners formed an integral part of the continent-wide genomic analysis published in the Science article, which gives a broader understanding of the evolution and epidemiology of the SARS-CoV-2 pandemic in Africa.  

Tackling COVID in Ghana, Botswana, Kenya and Rwanda

The contributions of the four TIBA partners to Africa’s COVID-19 control efforts clearly vindicates TIBA’s strategy of empowering African scientists to lead research that address local challenges. 

In Ghana, hosting the MinION sequencing workshop served as a springboard for my own institution, the West African Centre for Cell Biology of Infectious Pathogens.  Our lab’s sequencing capacity was further enhanced through a second NIHR grant, a Global Research Group award to the Sanger Institute, which is supporting malaria genomic epidemiology. 

The equipment, reagents and expertise built from these NIHR projects formed the basis for our ongoing SARS-CoV-2 genome sequencing work, which has generated the majority of data from Ghana deposited in GISAID and produced one of the earliest COVID-19 genomics publications from Africa (Ngoi et al 2020 Exp Biol Med).  We have now attracted further funding in support of its sequencing work from the Government of Ghana, Rockefeller foundation, Wellcome and the African Research Universities Alliance (ARUA).  

The Botswana Institute for Technology Research and Innovation (BITRI) in collaboration with the National Health Laboratory sequenced the first SARS-CoV-2 genomes in Botswana and confirmed the presence of the Beta variant, first detected in neighbouring South Africa. 

TIBA partners at the Kenya Medical Research Institute (KEMRI)-Wellcome Trust Programme in Kilifi have been leading SARS-CoV-2 sequencing work in Kenya. This team described the early introduction of SARS-CoV-2 in Kenya (Githinji et al 2021), circulation and establishment of local lineages (Agoti et al 2021) and COVID-19 transmission dynamics underlying epidemic waves in Kenya (Brand et al 2021)

TIBA-Kenya has trained 5 groups on SARS-CoV-2 sequencing within the country including a team from Rwanda. They have worked closely with the Ministry of Health to provide sustained genomic surveillance in Kenya, and these data have informed control measures and policy. They have generated more than 2,500 full-genomes from Kenya so far, some of which were included in our Science paper, and also supported sequencing efforts in Ethiopia, Sudan and the Indian Ocean islands through partnerships with Africa-CDC and WHO-AFRO. 

TIBA Rwanda arranged for further training in Edinburgh of two biotechnologists from the Rwanda National Reference Laboratory involved in epidemic surveillance.  They procured a MinION device and IT equipment required for sequencing from TIBA and Oxford Nanopore Technologies also provided flow cells and reagents. The team began SARS-CoV-2 sequencing and uploaded the first Rwanda sequences to GISAID in November, and in February 2021, the Rwandan Ministry of Health took ownership of the SARS-CoV-2 genomic surveillance. Thanks to TIBA, additional reagents and MinION devices were ordered, and today Rwanda Biomedical Centre and National Reference Laboratory is conducting routine sequencing of SARS-CoV-2. TIBA trained technicians were able to train others and have led the description of SARS-CoV-2 introductions into Rwanda (Butera et al, 2021, in Press, Nature Comms).

Current priorities and looking ahead

Genomic surveillance across Africa lags compared to other parts of the world and to date less than 43,000 genomes are available of which less than 20,000 can be considered as complete and high coverage. Of the available genomes, sequences from South Africa are proportionately large which makes it difficult to get a complete picture of SARS-CoV-2 diversity and skews analysis. TIBA partners are the largest contributors of sequence data outside South Africa.

Currently, several variants of concern are the leading source of new infections across the continent. Detailed analysis of the diversity of these variants within individual countries is vital, given the limited genomic sampling and low vaccine coverage. Based on the rate of mutation of the virus, we are likely to see a lot more vaccine-escape mutants that could scale back the gains that have been achieved and potentially cause large and deadly surges. 

Learning lessons from the COVID-19 pandemic, we believe that Africa needs to build on the momentum gained in genome sequencing and ensure that the continent is better positioned to respond to future epidemics.  Therefore, TIBA will be working with our funding partners to sustain the gains made and extend genome sequencing capacity to all TIBA partners. We have also identified additional partners in less endowed institutions in low-income countries, who can be mentored and supported to build research capacity in future. 

 

Author: Professor Gordon Awandare, Director, West African Center for Cell Biology of Infectious Pathogens, University of Ghana

His research focuses on the pathogenesis of Plasmodium falciparum in children, in particular the sialic acid-independent pathways of invasion and identifying novel receptors and ligands involved.