New portable DNA sequencers help East African farmers fight crop disease.

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

IMG_1012 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:

sdr 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 IMG_1527

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.

Tanzanian Team
Ugandan Team


  • 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).

 Find out more

For more information follow the blog at or @laura_boykin on twitter

You can get in touch with the team at, we would love to hear from collaborators and of course funders.


Laura Boykin, Cassava Virus Action Project/University of Western Australia:

Joseph Ndunguru, Mikocheni Agricultural Research Institute, Tanzania:

Titus Alicai, National Agricultural Research Organisation, Uganda:

Zoe McDougall, Oxford Nanopore:


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.

59 folders of data.

We have data!  Our run went for about 18 hours then we had a power cut – but we are ok and analyzing data and started another run! The team here at MARI is amazing. Massive shout out to Anders – who is back in Australia helping us lots and the nanopore team is doing the same – go team!



We are doing it!

Sunday we went and visited Asha Mohammad’s farm where her cassava yield is low due to cassava mosaic diseases, whiteflies and cassava brown streak disease.

We collected symptomatic leaves and whiteflies on the plants and rushed back to the lab. We extracted DNA from both cassava leaves and whiteflies.

Today the Nanopore shipment arrived and we used 4 cassava samples, from Asha’s farm, in the barcoding kit and started a run. With the real-time help from the nanopore team!

Fingers crossed! Our goal is go back and tell Asha what we found.

It begins!

Laura has made it to Tanzania and so it begins. The team here in TZ is ready!!

Laura, Calvin, Peter, Joseph and Charles  

Today we worked through several challenges including 1) shipping from the U.K. to TZ 2) internet outages and planning of experiments.

Shipping is a bit complicated but Charles here at MARI in TZ has made an awesome work flow to deal with it in the future see below-

New Note.png

We are awaiting the supplies to be cleared from customs…tomorrow- fingers crossed they were kept cold. The nanopore team has been great about helping around the clock.

Internet is down at MARI so we have opted to use my iPhone as a hotspot for the Macpro and use the Vodacom network because that has the strongest signal at MARI. Tomorrow we do some computer testing to make sure all the software is ready and up-to-date. Many thanks to Anders Savill from my team and Micheal Hall from Lachlan Coin’s group at UQ in Australia has made a cool new software –Streamformatics!!

Planning went well today.  We head to the field to meet farmers and collect infected material on Sunday and then extractions, etc


We are all so excited and looking forward to trying this technology!