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:

Mama Maina | Kenya | MinIT on battery

We did it! Three Tree labs in three countries (Tanzania, Uganda and Kenya) in three weeks.  In Kenya we went to visit Mama Maina and Mutunga’s farms near Thika, Kenya. In September 2017, we visited their farms and detected CMD viruses in both so we wanted to check the health of their plants with another rapid barcoding kit run. Our goal on this run was to decrease our time to results.  In Tanzania in Uganda it took us 4 hours from sample collection to results, this time we got the time down to 3 hours with great team work. Brenda Muga and Elijah Ateka were crucial in executing the Tree lab for Mama Maina and Mutunga. Interestingly, we found all the plants we tested were healthy- with no virus!  This is great news and will allow both farmers to sell their cassava sticks to others with no fear of spreading the virus.

We are now actively working on the crucial list of things we used to share with everyone and also analyzing all the results to present in a manuscript. Thank you to everyone who followed along- we are now ready to scale up our efforts.  We are always looking for partners who are willing to work for farmers. Thank you to Sam & Tom Industrys for shipping us a magnetic rack. Big shout out to the Nanopore team and Jo’s Zygem team who helped remotely.  Also a big thank you to Monica Kehoe and Anders Savill who helped from Australia.

MinIT on the battery:

Each Tree lab we started the run on the battery pack: found here.  To find it we searched “laptop power bank”.  The key for the power bank is to make sure it has not only USB inputs but also a power port and cable (see picture below with yellow circle around the cord you need). It ran on average 4.5 hours set on 16.5V.  Once the battery ran out we ran it from main power in a hotel room overnight if the hotel had no power (sometimes that was the case) we had a second power bank.  A better solution provided by Clive Brown at Nanopore is to have a input splitter so you don’t have to restart the device when the battery runs out.  The biggest challenge was trying to carry the battery, MinIT and the MinION in the car- typically we used a cardboard box-but not too small because once the MinION overheated because we put it in a cooler box.

MinIT and airport security- a few times the airport security people wanted to know what it was- we made sure to have a battery in the carry-on to power it up.  We explained it was used for diagnostics of sick plants AND had photos of us using it in the field so they could easily see the use.

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Uganda | MinIT | Sarah | Power

Uganda: Round 2 taking the tree lab to the farmer. This time we followed up with our farmer Naomi- turns out she has moved back to her village up north BUT her cassava fields were in good hands as her sister Olivia was looking after them and the harvest was massive.  One farmer at a time we will transform the food security space.

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Naomi’s cassava- 9 months later. IMPACT.

We arrived at the lab to find no power or internet – for the entire week- so it gave us the chance to test the infield diagnostic equipment with the Ugandan team!  All went well.  We set-up another tree lab to help farmer Sarah and her beautiful family including her daughter Sandra. They enjoyed watching the DNA extraction, library prep, sequencing followed by some quick bioinformatics.  Happy to report Jo’s DNA extraction machine coupled with the minION and the MinIT make the perfect mobile lab. On the spot diagnostics. Proud. Very proud.  We are now in Kenya and will do it all over again here. Pictures are worth a thousand words- see below for the magical moments in Uganda.

Asha/MinIT- the mini supercomputer/Lab under a tree

Two new additions to the crew. We had Dr. Jo-Ann Stanton from New Zealand bring her PDQx (pretty damn quick extraction) machine to test in the field and we had Dr. Ibrahim Mohammad from Kebbi State University in Northern Nigeria. All gathered around getting technology and science to farmers to diagnose what is killing their cassava and to ID the whitefly species in the farmer’s fields.

Asha:

We have just finished our 10 days with the Tanzanian team.  Our highlights were visiting Asha’s farm after 9 months- she has gone from 0 tonnes/hectare to 35-40 tonnes/hectare. See our first visit here: https://vimeo.com/233953210. She was given two varieties of cassava to grow in September 2017 – Kiroba & Mkuranga.  Prior to this she and her group were growing local varieties.

 Asha now has a new problem- she needs a market to sell her extra cassava because her family is food secure… and so are the families of the group members. This is a good problem to have and now we will work with Asha to navigate selling her excess.  The power of science and technology was witnessed first hand.

The MinIT (aka the mini-supercomputer) in the lab:

Step one was to get power banks that would work in the field. We bought two laptop power banks – within regulations of the airlines because we are traveling between countries (Tanzania, Uganda and Kenya). Another key was to do a test run before we took it into the field- we did this with Clara- a PhD student from Sokoine University of Agriculture- at Mikocheni Agricultural Research Institute- our lead node in TZ. Clara is studying African Swine Fever- a DNA virus so we thought this was a good test before heading into the field to test cassava. She did a DNA extraction and we tested out the MinIT. Rich from Oxford Nanopore sent us a couple of pages of quick start guides and away we were. In addition, Chris S. gave us lots of good advice on the device and saved us a few times! We connected to it via wi-fi and on there is a MinKnow version that we used to QC the flow cell- all that was fine.  When we went to start the run the software on the MinIT wasn’t giving us the option to select the kits so we immediately switched to starting the MinIT via the MinKnow software on the laptop and telling it to connect to a remote device (the MinIT connected via wi-fi).  The run started and immediately the MinIT started basecalling and keeping up with reads being produced! We let that run for a day.

MinIT in the field- Musoma, Tanzania:

Our BIG test was to sequence IN THE FIELD.  So we set out to the Mara Region of Tanzania where the cassava team has been working with farmers in the region for 4 years- giving them clean planting material, training extension workers, training farmers about planting, etc.  Our mission here was to 1) test their improved varieties for virus 2) test whiteflies for virus and to ID species and 3) introduce the devices to the government officials. All were accomplished- more on this soon. BUT we did it. We did a DNA extraction of 12 samples, library prep (SQK-RBK004) and data analyses all while farmers waited and we gave them immediate feedback on what to do next. EPIC day.  Full of challenges. We used local blast databases installed on a laptop for both the cassava viruses and whiteflies and once we had some .fastq files we imported them into Geneious and blasted them and we were able to see what viruses were in the whiteflies and the cassava leaves. Both Jo’s device and the MinIT lived up to the hype- couldn’t have done it end to end without them.  Power of diversity.  Huge shout-out to the MARI team- Peter, Charles, Deo and Joseph in addition the farmers who trust us to do this.

We are now in Uganda and going to sit with Dr. Titus Alicai’s team to plan our next lab under a tree.