Yasss! The MinIT has arrived- DATA, DATA, DATA.

We are so excited to have in our possession the very first MinIT!  Big shout out to the Oxford Nanopore team for working so hard to get this to us before we head out next Tuesday.  Super excited to use it in the farmers’s field to tell them what viruses and vectors are causing such huge yield loss. Stay tuned y’all.

Tanzania, Uganda and Kenya- Round 4

We are gearing up for a 3 country expedition. Super excited to have Dr. Jo-Ann Stanton from University of Otago, New Zealand joining us to try out her amazing point of care devices in the field!  Jo and Laura met this past March when Laura visited Genetics Otago– many thanks to Julia Horsfield and Amarni Thomas for the connection!

Our plan is to follow-up with Asha, our farmer in Tanzania who is featured here. Her improved cassava has been in the field for 9 months and we celebrate her harvest with her and the village. True impact! We have many exciting things planned for Uganda and Kenya.  In addition, we are planning to do more rapid barcoding of infected material and also more capacity building throughout. We are also awaiting a very special package from Oxford Nanopore that will make our in-field data analyses much much easier! Stay tuned for updates.

Update from Njombe, Tanzania!

Report from Dr Ndunguru in Njombe, Tanzania : 107 farmers turn out to harvest the cassava variety Mkombozi which does well at low temp (16-18C) and is resistant to the CMD in the area. Massive yields and farmers are so happy. Impactful science

The first time nanopore has been used to sequence plant viruses!

A big day for the team! Our preprint is now available- Real time portable genome sequencing for global food security

‘For the first time globally, the MinION portable pocket DNA sequencer was used to sequence whole plant virus genomes. We used this technology to identify the begomoviruses causing the devastating CMD which is ravaging smallholder farmers crops in sub-Saharan Africa.’

Bleeding edge technology- East African scientists leading the charge to help farmers.

Updates from the CVAP team!

  • Our TZ node won a prize at the World Government Summit Awards in Dubai UAE for applying Nanopore sequencing for smallholder farmers – Congrats. The team was on Tanzanian morning TV.
  • We successfully trained scientists at University in Eldoret and JKUAT on bioinformatics and running the MINion. Many thanks for the Crawford Fund for supporting the work and also the 69 people who donated to our crowdfunding page!  Please see Professor Elizabeth Njenga and Dr. Jayne Binot describing the course and what it means to the team in Kenya [sorry about the wind, I’m not a video pro]

  • And we are excited to be invited to give a talk at the London Calling Meeting in May! We will see you all there!Screen Shot 2018-03-27 at 12.45.18 PM
  • Special videos to our crowdfunding supporters: (we promised we would shout their names form the mountain in Kenya) .


A very challenging two weeks but we did it, we made it. We have data for 12 cassava plants – some showing symptoms and some were not.

Dr. Naomi Bissem’s tweet says it all:

Screen Shot 2018-03-04 at 9.22.00 PM

Details: We learned A LOT on this trip.  Shipping was a challenge.  We discovered FedEx froze our flow cells- and this is no joke.  It ruined all the flow cells but luckily Nanopore sent us  new flow cells (as per the suggestions below) via DHL.  We learned that that little gray pad on the flow cell is super important for temperature control (thank you twitter for helping real-time). We learned that the priming of the flow cell is important and if your library isn’t going in the spot-on port to add more priming mix to the flow cell to get things moving.  We learned that power is not a given.  We should have had a battery back up on the machine we were using.  We also learned once (actually 3 times) when the power goes off you can quickly start the machine running and it keeps sequencing.


The team: I also learned the team from University of Eldoret has some serious tenacity. They boarded a bus Thursday night upon hearing we received the shipment- drove 6 hours- and we began preparing the library Friday morning, started the run (3 times with the power cuts) and then got back on the bus and drove back to Eldoret. In addition, Charles Kayuki, from Mikocheni Agricultural Research Institute (MARI)  joined us for the second week at JKUAT – he was a valuable resource as he has completed runs on his own in Tanzania. Anders Savill in Australia was on-call and dealing with us at all hours- thank you Anders. Plus Angelica and Zoe from Nanopore were amazing at facilitating so many things on that end. Finally, the JKUAT team lead by Professor Ateka- was invaluable, fierce, dedicated and downright amazing. Elijah Ateka, Brenda Muga, Sam Maura, and Benson – Asante Sana for relentless fight to get this test done.


The farmers: Rose, from Eldoret had CMD symptomatic plants.  We tested her plants and Prof. Ateka provided her the virus resistant cassava. The team from Eldoret took the cuttings to her and she is on her way.  We also visited two other farms, Mama Maina and Mr. Lungo Mutunga’s farm in Thika, Kenya. We are awaiting the results of the run and will advise them later this week.


Prison Visit: While we waited for the flow cells to arrive we visited Langata Women Maximun Security Prison to conduct a cassava pest and disease training for inmates and farm managers.  We feel very strongly empowering all farmers is at the core of our movement. This was a very special day and the team plans to go back and plant virus-free cassava with the inmates on the prison farm.  Outreach matters.


NO! The flow cells were dead. Suggestions for labeling the box.

Ok, so we had ZERO pores on our two flow cells.  We suspect our flow cells were frozen in customs. Why? 1) It’s the first time they have been shipped here (so these items were not in the Kenyan customs officials database) and 2) We feel the labeling on the Nanopore box needs a bit of improvement when shipped to Kenya (and E. Africa in general). So here are our suggestions:

On the BOX:

1.     Ship separate boxes for each temperature (customs can’t open the box to separate).

2.     In large font on the box  “Store Freeze -20C” OR

3.     In large font on the box  “Store Fridge 2-8C”

4.     Highlight the temperature in the paperwork
5.     Put recipients phone number on the outside of the box

Paperwork taped ON THE BOX:

1.     Clearly state the material is not poisonous or for human consumption

2.     Clearly state it has no resale value and is for research only
We have another shipment on the way. Let’s hope we get it quickly and with new labelling.

We got the goods!

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!