Democratic Republic of the Congo and Sierra Leone- #sequencing4farmers & #poresafari

Democratic Republic of the Congo: September took the team (Dr. Jo-Ann Stanton and Dr. Laura Boykin) to Democratic Republic of the Congo to meeting with long time collaborator Tony Bakelana (INERA)- we are working to uncover the causal agent of the cassava root necrosis in the western parts of DRC. We also teamed up with Dr. Gerrye Mubungu (U of Kinshasa) and Dr. Hugues Abriel and Oxford Nanopore (Iain MacLaren and Charles Kayuki) to put on Pore Safari #2 – where we trained over 60 students in over 3 days.  It was an epic 3 days.  Soon we shall publish the results of the sequencing on the farmer for the Lukuakua farmers.

Sierra Leone: The second week of the trip took us to Sierra Leone at the invitation of His Excellency President Dr Julius Maada Bio and his chief Innovation Officer, Dr David Moinina Sengeh- who is also a Senior TED Fellow along with CVAP’s Dr. Laura Boykin. Laura met the pair at TED 2019 where HE gave a TED talk on innovation to drive change. More about this meeting can be found here. We conducted some research on AI cassava disease recognition with David’s DTSI team and Dr. Alusaine Samura- who is a cassava disease expert. Stay tuned for those results!

In addition, we carried out training of 60+ scientists on the Oxford Nanopore technologies – flow cell loading, library preparation and we generated sequence data.

News reports on the visit can be found here and here.

Brenda presents at the UN Solutions Summit in Nairobi, Kenya.

Team member Brenda Muga presented our solution to ending hunger at a United Nations event in Nairobi Kenya.

From the event:”Approximately 800 million people rely on the Cassava plant, as a source of food and/or a source of income. But Cassava is being devastated by two viruses across East Africa, both transmitted by the whitefly: Cassava mosaic disease and Cassava brown streak disease. Brenda Muga, a young scientist, and her team at the Cassava Virus Action Project (CVAP), have the audacious goal to save the cassava plant and, in the process, build infrastructure and scientific capacity to handle any crop disease outbreak or pandemic in East Africa. Using the latest technologies, such as pocket DNA sequencing and supercomputing, CVAP can almost instantly diagnose the health of crops in the field — a process that used to take 3 months. CVAP also strives to achieve equity in science, as team members are based in the national labs of each country, ensuring that the voices of local scientists are heard. Through these paradigm shifts, CVAP aims to positively impact the lives of 10 million farmers and their families within the next 6 years, and equip East Africa with the tools and resilience needed to stop outbreaks of deadly pathogens.”

 

We are one of Fast Company’s World Changing Ideas for 2019!

We are so excited to announce that The Cassava Virus Action Project has been named a finalist in Fast Company’s world changing Ideas for 2019!

Watch a new video about our work here: https://vimeo.com/329068227!

Now in its third year, the World Changing Ideas Award showcases 17 winners, more than 200 finalists, and more than 300 honorable mentions, with Health and Wellness, Education, and AI and Data among the most popular categories. A panel of eminent judges selected winners and finalists from a pool of more than 2,000 entries, such as Food, Energy, and Developing World Technology.

About the World Changing Ideas Awards: World Changing Ideas is one of Fast Company’s major annual awards programs and is focused on social good, seeking to elevate finished products and brave concepts that make the world better. A panel of judges from across sectors choose winners, finalists, and honorable mentions based on feasibility and the potential for impact. With a goal of awarding ingenuity and fostering innovation, Fast Company draws attention to ideas with great potential and helps them expand their reach to inspire more people to start working on solving the problems that affect us all.

Our Entry-The Cassava Virus Action Project:  Our world changing idea is to save cassava, a plant that feeds 800 million people globally by using pocket DNA sequencing & supercomputing & data analytics all while increasing diversity, equity and inclusion in STEM. 1 billion people live in extreme poverty and the majority of them are smallholder farmers. The world has all the tools to end hunger. Our team has the world changing idea to use these tools to save cassava, a plant that feeds 800 million globally and, in the process, we will build infrastructure and scientific capacity to handle any outbreak or pandemic in east Africa. And the bonus- this will bring equity to science at a pace never seen before. The highest tech solutions will be driven by east Africa for the globe. Now that’s a world changing paradigm shift long overdue. The Cassava Virus Action Project’s (CVAP) mission is to use the latest technologies, such as pocket DNA sequencing and supercomputing, to positively impact the lives of 10 million farmers and their families in the next 6 years. The project plans to scale its work with farmers by engaging with an already established network and by building new connections to the technology and medical hubs in the region.

The Cassava Virus Action Project is a network of researchers, farmers and technology industry people collaborating to use genomic technologies to improve the management of these Cassava viruses. We have a not-for-profit fiscal sponsor called Multiplier in the USA, which accelerates impact for initiatives that protect and foster a healthy, sustainable, resilient and equitable world. Our goals are to 1) Increase plant yields for farmers for 10 million people in 6 years and 2) open 3 hi-tech labs in the region that can handle future outbreaks and pandemics in the region. If scientists and technologists in east Africa analyze the DNA of the virus, quickly and close to the crop or host, you could understand what virus it is and decide what action to take. We will empower local communities to make decisions that maximize their crops while also minimizing the spread of these pathogens. Bringing the strongest women on the planet, the smallholder farmers in East Africa, into the light will only help the globes plight for food security. Direct rapid DNA/RNA sequencing of infected material on-the-spot or near sample collection sites turns this conventional paradigm on its head by taking the laboratory closer to farmers’ fields. This reduces overall costs and gives crop protection officers and farmers in rural communities’ information critical for sustainable crop production and management of pests and diseases, thus ensuring food and income security for millions of Africans.

Help us scale: https://multiplier.org/project/cassava-virus-action-project/

More sequencing for farmers in Tanzania

February 2019 we had a informal training session at Dr. Ndunguru’s new research facility TARI-Selian in Arusha, Tanzania. This trip we ran our first Oxford Nanopore plant and vector diagnostic clinic! We had scientists in the region bring infected plant samples and insects they were interested in sequencing including wheat, barley, maize, beans, fall army worm, whiteflies and more. We used a the Qiagen DNeasy plant kit for extractions this time [shout-out to Dr. Monica Kehoe for the help] as we are waiting for the PDQeX to be available and Chelex for the insects. We had success but it is up to those researchers to tell their stories so we shall leave it at that. The data analyses was much harder because we had so many hosts and also we had no idea what we would find so we partnered with Associate Professor Lachlan Coin and his team who have developed a cool new cloud solution. Charles Kayuki was an excellent training and did a great job with instructions in Kiswahili! See below.

We also had the great fortune of having a meeting with Honorable Christophe Bazivamo who is the Deputy Secretary General of Product Services for the East African Community. He and the team were very impressed with the project and invited us to Kampala, Uganda to present our work to the East African Community regional consultations on the draft EAC SPS regulations and SOPS validation meeting in Kampala, Uganda on 26-28th Feb, 2019.  Dr. Sseruwagi and Dr. Laura Boykin attended the meeting and presented the work for the team. Everyone was very receptive.  Further engagement is ongoing.

And finally, we had the great honor to be featured in three news items below:

PNAS 

Cray

KENET

Some pictures from the training in Arusha, Tanzania: