Investigating the role of bushmeat in the transmission of zoonotic diseases in Tanzania

Research conducted by the Biosciences eastern and central Africa-International Livestock Research Institute (BecA-ILRI) Hub in collaboration with National Health Laboratory of the Tanzania Ministry of Health and Social Welfare; Nelson Mandela African Institution of Science and Technology (NM-AIST); Sokoine University of Agriculture; Tanzania National Parks; Tanzania Wildlife Research Institute; Frankfurt Zoological Society; and Pennsylvania State University.

An outcome of the BecA-ILRI Hub’s Swedish funded initiative to strengthen infrastructural and human capability at NM-AIST, was the awarding of a grant to the institution by the US Defense Threat Reduction Agency.

The NM-AIST School of Life Sciences and Bioengineering and a consortium of partners including the BecA-ILRI Hub received a grant to investigate the role of bushmeat in the transmission of six pathogens between animals and humans in Tanzania.

An interdisciplinary and multi-institutional team of scientists from Tanzania, Kenya and the US are using state-of-the-art techniques to map the distribution of anthrax, ebola, marburg and monkeypox viruses as well as Brucella and Coxiella in bushmeat in Tanzania. The team assesses the biological risk and potential for impact on human health from these diseases.

The BecA-ILRI Hub provides capacity building, expertise and technology for the microbiome component of the project using the genomics platform. During a week-long workshop facilitated by the BecA-ILRI Hub at NM-AIST, Francesca Stomeo provided training on the theory and practice of the genomics pipeline to be used in the project.

Read more about the bioscience research and innovations that underpin development outcomes in the BecA-ILRI Hub 2016 Annual Report.

Joyce Nzioki (left) and Fracnesca Stomeo at the Earlham Institute in Norwich, UK

From 1-13 July 2017, capacity building scientist Francesca Stomeo and I visited the Earlham Institute in Norwich, UK. Our mission was to explore ways of strengthening the budding partnership between the BecA-ILRI Hub and Earlham Institute as well as to gain knowledge that will improve the Hub’s genomics and bioinformatics platform.

We had an intense one and a half week of meetings and interaction with the institute’s genomics and bioinformatics specialists, with guidance of our hosts Anthony Hall, head of plant genomics and post-doctoral scientist Jose de Vega. There was much to learn about different aspects of genomics and bioinformatics, particularly in terms of lab and bioinformatics protocols and systems.

It was very exciting to share experiences on our research and training opportunities, and make potential connections for joint activities in the near future. The discussion we had with the project leader-bioinformatic algorithms, Bernardo Clavijo was invaluable in planning for the BecA-ILRI Hub annual advanced bioinformatics workshop that will take place in October this year. I am really glad that Clavijo will be among the trainers for that workshop.

Discussions on work by national agricultural research system (NARS) research fellows conducted at the BecA-ILRI Hub highlighted potential areas of collaborative research to enhance food safety and security in Africa including: improved conservation of fish, understanding drug resistance in Salmonella, plant transformation and exploiting various under-utilized African crop species. We were also challenged to consider introducing the portable Oxford Nano Pore sequencing technology to serve our partners who may not be able to purchase the bigger high through put sequencing machines.

From the visit to Earlham Institute, I saw a clear need for improved bioinformatics capacity to fulfil the potential of modern biosciences in Africa. Bioinformatics training—a key component of the BecA-ILRI Hub’s remit—is central to the training conducted at the Norwich Research Park (NRP), of which the Earlham Institute is a partner. We had fruitful discussions on strategies to empower a cohort of bioinformaticians in Africa with hands-on training in 2018.

I look forward to many joint research and training activities with scientists in Earlham Institute starting with the bioinformatics workshop in October!

The sequencing facility at the Earlham Institute in Norwich, UK

About the author:
Joyce Nzioki is a bioinformatics analyst providing bioinformatics support to various on-going genomics projects at the BecA-ILRI Hub. She holds a Masters in Bioinformatics from Rhodes University in South Africa and a Bachelor’s degree in Biomedical Technology from the University of Nairobi, Kenya. Through her MSc studies, she gained skills in working in a Linux environment, Python programming, mathematical and statistical applications to biology and bioinformatics (R and Matlab), structural bioinformatics, genomics and proteomics.

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Aphids, leafhoppers and whiteflies are responsible for the spread of diseases causing significant crop yield losses globally. On 5 July 2017, the Biosciences eastern and central Africa-International Livestock Research Institute (BecA-ILRI) Hub hosted a symposium to explore ways in which the knowledge of plants, disease-causing organisms and their vectors can be used to combat devastating crop diseases in Africa.

Stephen Runo of Kenyatta University (left) with JIC scientists Beccy Corkill, Olu Shorinola and Sam Mugford (photo JIC/Matt Heaton)

In sub Saharan Africa, the aphid-transmitted bean viruses—bean common mosaic virus (BCMV) and bean common mosaic necrosis virus (BCMNV)—cause up to 100 percent losses for smallholder bean farmers. Growers of cassava—a staple food for over 250 million people— experience losses of up to 23 million tonnes annually across Africa due to disease caused by whitefly-transmitted Cassava mosaic viruses.

In the face of increased regulations on the use of pesticides, a better understanding of the plant-microbe-vector interactions could lead to the development of urgently needed bio pest-controls. The July forum brought together researchers from the BecA-ILRI Hub, Kenyatta University, International Institute of Tropical Agriculture (IITA), Auburn University and North Carolina State University based in Africa; and the John Innes Centre (JIC) from UK.

From left to right: Josiah Mutuku (BecA-ILRI Hub), Olu Shorinola (JIC), Steven Runo (Kenyatta University), Beccy Corkill (JIC) and Sam Mugford (JIC) at the BecA-ILRI Hub greenhouses (photo: JIC/ Matt Heaton

The symposium was held under the Alliance for Accelerated Crop Improvement in Africa (ACACIA) initiative—a new initiative established to harness diverse research efforts for hastened crop improvement in Africa.

Read full story: Deciphering Plant-Insect Interactions on the ACACIA website.

Read about the ACACIA initiative: New initiative to accelerate crop improvement for food security in Africa

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Performed by the BecA-ILRI Hub staff, research fellows from African national programs and international collaborators, this 25 minute skit sheds light on how technology, partnerships and increased research capabilities of national agricultural researchers and institutions can bring about agricultural development in Africa.

The play dramatizes the role of the BecA-ILRI Hub and its national and international partners in bridging high-end research with practical solutions for smallholder farmers. Established as an African centre for excellence for agricultural biosciences, the BecA-ILRI Hub supports African national agricultural research institutes and universities enhance in harnessing bioscience technologies for sustainable agricultural development in Africa.

Harnessing the diversity of native livestock in Africa is becoming a pressing need as continual changes in the environment exert pressure on small holder livestock farmers. The higher temperatures and changing rainfall patterns are contributing to the increased spread of existing vector-borne diseases and the emergence of  new diseases as well affecting the feed production.

Small ruminants play a significant role in livestock production systems throughout the wide range of agro-ecological regions in Africa. For many rural farmers, they are a critical resource of nutrition and income, and goats in particular are more resilient and adapted to different husbandry conditions. It is well documented that genetic variation in ability to various infections and diseases as well as to adapt to harsh environments with higher temperatures and less water, exists between and within different breeds of goats.This adaptation is especially evident in indigenous breeds, but gaps still exist in the knowledge available.

The “Harnessing genetic diversity for improved goat productivity” project is focused on bridging this knowledge gap by helping farmers take advantage of the best genetic resources locally available. Our strategy involves working closely with the goat keepers, traders, policy makers and all other stakeholders so that there is collective ownership of the existing problems and in the approach to finding solutions. Through the innovation platform (IP) system, the project is drawing from the existing indigenous knowledge, receiving guidance in terms of farmers’ actual needs and preferences and establishing effective channels that act as vehicles for information on research findings and promotion of sustainable livestock keeping practices.

Already in Cameroon, one regional IP in Kouoptamo (West Highlands) has identified high fecundity as a desirable trait in their goats and are promoting their animals as high value breeding stock for proven twinning ability. Additionally, as a result of close engagement with the project through the
Cameroon National goat IP, the Ministry of Livestock, fisheries and animal industries has recognized the importance of goats and small ruminants as an important resource to grow the country’s rural economy and has started a program to revitalize three small ruminant breeding and multiplication
stations in different agro-ecological regions.

Our counterparts in Ethiopia have established a community based goat breeding initiative where a group of 50 farmers have formed a cooperative society to drive the breeding activities. The cooperative members brought their goats for selection to form the next generation of goat parents in their village and in the neighbouring villages as well.

I see this active participation by communities as a very exciting and practical way of doing research. Through community involvement, the project has been able to stay relevant and ensure that good science supports the things that are most relevant to Africa’s development.

The visit to ILRI specifically aimed at identifying relevant and specific international public and private sector program concepts and strategies that are applicable, can be refined and adapted to strengthen the genetic improvement, enterprise development, and research and development of the National Carabao Development Program.

While at ILRI, the PCC team met with Dr. Rob Skilton, Team Leader, Capacity Building at the BecA-ILRI Hub who  gave them an insight to the different avenues of capacity building, knowledge transfer and  sharing of facilities that are being used to solve some of Africa’s key agricultural challenges.

The full article can be accessed here: http://www.searca.org/index.php/news/1454-searca-pcc-institutional-benchmarking-activity-in-kenya-begins-smoothly

Gity Berhavan, Senior Research Advisor/First Secretary: Regional Research Cooperation, Embassy of Sweden in Kenya during an interview at the BecA-ILRI Hub (photo credit: BecA-ILRI Hub/Tim Hall)

Sweden’s strategy for development cooperation with Africa, especially in the area of research, is to align itself with the African agenda. For example, the African Union’s New Partnership for Africa’s Development (AU/NEPAD) Comprehensive Africa Agriculture Development Programme (CAADP) agenda is to increase the productivity of the food and agricultural systems in Africa.

Partnering with the BecA-ILRI Hub (or BecA) is a strategic way of tapping into the wider African science agenda. The BecAILRI Hub is an African initiative that responds to this agenda by bringing together different national agricultural research institutions in collaborative research based on regional and national priorities, for the improvement of livestock and crop production.

By supporting BecA, the Swedish government is able to provide funding to increase the capacity of an array of African institutions to conduct high end agricultural research. A case in point BecA’s programme to increase the use of bioinformatics to mine genomics and metagenomics data for the development of disease diagnostics tools. Through this programme, the knowledge and capacity in bioinformatics which is already at Hub is being extended to other institutions in the region, ensuring the sustainability of research in that area. The African Biosciences Challenge Fund (ABCF) is another exciting programme which is giving early career scientists in Africa access to training and skills that will enable them to design and lead bigger research projects on their own.

The highlight of the review, however, has been getting acquainted with the kind of research and capacity building alliances the BecA-ILRI Hub is building that are not limited to ‘south-south’, ‘north-south’ but also ‘south-south-north’ collaborations. These broad partnerships are what 21st Century research needs in order to find timely solutions to the challenges of global food insecurity.

Going forward, we would like to see the BecA-ILRI Hub engage more with policy makers and institutions responsible for the development of national Masters and PhD programmes curriculum development. A paradigm shift from training scholars for employment, to training scientists who will create jobs through innovative research will greatly accelerate development in the region.

We would also wish to see the constitution of the BecA advisory panel as laid out in the new BecA-ILRI Hub Business plan for 2013-2018. This panel will play a very critical role in providing dynamic strategic direction in the selection of projects and partners in the future.