Elijah is a star!!! He freed the box from customs. And now we are on our way. We visited Rose – a farmer here in Eldoret, Kenya she has a small plot of cassava and we suspect it is infected soon we will know!
The team here at University of Eldoret has kindly hosted us in their biotechnology lab for the DNA extractions.
Tomorrow we do the library prep & start the nanopore run!
Our things have been stuck in customs for 2 weeks. Elijah has driven 5 hours one way (back to Nairobi from Eldoret) and is planning a sit-in at the customs building to get our supplies. Then he and Benson are driving another 5 hours back to Eldoret! The shipping struggle is real. If anyone has connections, solutions, ideas about making this easier please get in touch. We are determined to do this on Thursday with the class at University of Eldoret. Wish us luck.
2 weeks left before we leave. The shipment from Nanopore is on it’s way to Prof. Ateka in Kenya. We have ordered two of the R9.4 flow cells – to go with the 1 new Rapid Barcoding Kit RBK004. It was advised to use the 9.4 flow cells instead of the 9.5 so that is what we will do! Also the Anders Savill has been preparing the MacMini we are taking with us to do the work and then leave at JKUAT. The third time around things are falling into place. It’s all very exciting.
February 19, 2018 we begin the journey to bring Nanopore sequencing to farmers in Kenya. Professor Elijah Ateka and his team at JKUAT will be hosting and driving the activities! We will also put on a training course at El Doret University many thanks to crowdfunding & The Crawford Fund.
Dr. Laura M Boykin has won the international Gifted Citizen Prize for 2017 in Puebla, Mexico as part of the La Cuidad de las Ideas Festival awarded November 18, 2017. Each year the Gifted Citizen Prize is given to the best social entrepreneurship project that has the ability to benefit 10 million people over the next six years. This international prize honors the passions of those that seek to develop real solutions to humanity’s most pressing issues. Those that are recognized with the Gifted Citizen Prize are celebrated for their ability to defy contemporary paradigms and generate pragmatic answers to the most urgent global needs. This year there were over 1700 applications and the top 32 were invited to Mexico to compete in the competition and Dr. Boykin came out on top and won the prize of one million pesos.
She presented the team’s latest project, The Cassava Virus Action Project, which is a network of researchers, farmers and industry people, collaborating to use a pocket DNA sequencer to improve the management of cassava viruses in east Africa. For the first time in September 2017, farmers struggling with diseased cassava crops can take immediate, positive action to save their livelihoods based on information about the health of their plants, generated using a portable, real-time DNA analysis device. The team now plans to expand the project; 800 million people worldwide depend on the threatened cassava crop. The project aims to reduce the risk of community crop failure and help preserve livelihoods.
The CVAP team will use the prize winnings to launch a node of the project in Kenya in early 2018 and the overall goal of the project is to scale up across the continent and touch the lives of millions of farmers in east Africa.
Drs. Ndunguru, Alicai and Tairo attended the 2nd annual meeting of the BMGF funded project entitled “West African Virus Epidemiology (WAVE)” last week. At the meeting the team presented the work of CVAP to the WAVE team. This is a big step in bridging east and west Africa in the fight against these devastating cassava viruses. The plan is to move forward as a continent with the Nanopore sequencing.
15th September 2017, Tanzania, Uganda, Perth, Oxford. New portable DNA sequencing technology has for the first time been deployed in East Africa to help collaborating scientists and farmers fight the devastating impact of crop disease.
For the first time, farmers struggling with diseased cassava crops can take immediate, positive action to save their livelihoods based on information about the health of their plants, generated using a portable, real-time DNA analysis device. The team now plans to expand the project; 800 million people worldwide depend on the threatened cassava crop. The project aims to reduce the risk of community crop failure and help preserve livelihoods.
Cassava, a carbohydrate crop from which tapioca originates, plays a critical role in agriculture in developing countries. 800 million people depend on it worldwide as their primary food staple. It is currently being devastated by several viruses causing two diseases; ‘Cassava mosaic disease’ (CMD), which led to major famines in the 1920s and 1990s, and ‘Cassava brown streak disease’ (CBSD), an epidemic of which is rapidly expanding in eastern Africa.
Both diseases, carried by the whitefly, prevent normal growth of cassava plants. This leads to significantly reduced harvests or even complete losses by farmers. Both viruses, carried by the whitefly, make the plant inedible and unsellable, and their presence means the crop must be destroyed to stop its spread.
Oxford Nanopore’s portable MinION DNA sequencer was used to identify which strain of virus was destroying the cassava crops of farmers in Tanzania and Uganda as part of a collaboration of scientists and farmers, known as the Cassava Virus Action Project (CVAP). As MinION delivers the information in real time (compared to the usual three months), farmers were able to take action much faster. One was advised to destroy the crop and plant a different variety that is more resistant to the virus for example.
“We have shown that pocket DNA sequencers can benefit rural farming communities who would not normally have access to such technologies as they are usually more expensive and slower,” said Joseph Ndunguru, co-PI, and Director of the Mikocheni Agricultural Research Institute in Tanzania. “Even within this pilot project, through rapid and accurate identification of viruses, farmers can now understand which crops to plant, which are resistant to a particular virus species/strain. This is key to attaining durable disease resistance and improved crop productivity. This technology also is easy to use, making it possible to do without major infrastructure and staffing.
Titus Alicai, co-PI, Research Programme Leader with the National Agricultural Research Organisation, Uganda, said “We were successful in field application of the powerful mobile MinION sequencing tool for rapid, precise, unbiased detection and identification of viruses in farmers’ cassava fields. This eases monitoring of field virus strain populations which is essential for timely control actions such as production of clean planting material and development of resistant varieties.”
Laura Boykin, co-PI of the project and scientist at the University of Western Australia added “We now plan to expand the project within Tanzania and Uganda, and to collaborate with other countries that haven’t yet been affected by Cassava whitefly viruses, like Thailand and Brazil. If better strategies are not found to deal with this crop disease then millions of people could be affected – we need to think about economies as well as individual families
The MinION, which weighs only 100g and can be used in any location where it can be plugged into a laptop or PC, was used to sequence both cassava plants and whiteflies thereby identifying the precise strain of the virus that was present as well as the variety of cassava the farmer was growing.
The cassava disease diagnostics project was co-funded by the Bill & Melinda Gates Foundation and by the UK’s Department for International Development, and served as a solid foundation for CVAP.
Case Study 1, Tanzania:
Asha Mohammad’s farm in Bagamoyo has low cassava yields.. Asha will soon have her Cassava farm back on track with new information about the viruses and plants. Rapid, local DNA analysis gave her the insight she needed to recover her crop. She now plans to share the knowledge she has received with her 10-member women’s cassava farming group and they plan to share the knowledge with other farming groups- spreading knowledge far and wide.
Case Study 2 Uganda:
Farmer Naomi Kutesakwe in Wakiso is also suffering from low cassava yields. Upon inspection, her cassava crop was observed to be severely affected by cassava mosaic disease, cassava brown streak disease and whiteflies. The team collected samples and sequenced them with the portable DNA sequencer. In 48 hours returned to provide her vital information to help increase her yields in the future
Capacity building was another crucial part of our study – we now have ten users of the Oxford Nanopore MinION in the region and the hope is to scale this up quickly to help in the fight to feed the population – especially the most vulnerable, the smallholder farmers globally. The teams in Tanzania and Uganda will remain on the front lines of fighting these devastating viruses and we are excited to utilize these technologies for other pests and diseases.
Both CMD and CBSD have seriously reduced yields across the African continent, often forcing farmers to abandon their fields.
It is estimated that between $2-3 billion (USD) is lost annually as a result of CMD in Sub Saharan Africa (Scholthof et al, 2011)
CBSD caused estimated crop losses in Tanzania of between $35-70 million USD/year (IITA, 2006).
The Ugandan team is ready. We arrived late Thursday night – had a planning meeting Friday morning and we were in Naomi’s field by 2pm Friday. We then started a CTAB extraction and began finding a suitable computer. The computer was our biggest challenge. We first started with a MacMini 2TB hard drive 16gb ram – after 6 hours of struggling with help from both Anders in Australia and Monolina from nanopore we had to leave because the generator was going off. Monolina found out the older Mac does not have the drivers for the minknow. So we found a windows machine with 300gB of space – no SSD drive- but we are using it anyway. Yesterday we started the run- and now we wait!
Oh and massive shout out to the delivery magicians- Norman Mugisa & John Mayombwe.