East African scientists turn to gene sequencing against 'Ebola of plants'

Story highlights

  • Whitefly-borne disease destroys over $1 billion worth of cassava
  • Fresh outbreak inflicts dire humanitarian crises
  • Scientists turn to gene-sequencing technology to fight disease

(CNN)Almost a billion people around the world rely on cassava as a staple food. The root vegetable is a versatile and calorie-rich crop that is resilient enough to thrive in harsh climates.

But the cassava has no defense against a tiny insect that is decimating crops across East Africa, with dire economic and humanitarian consequences.
    The whitefly carries two viruses that together destroy over $1 billion worth of cassava in Sub-Saharan Africa each year. Cassava Mosaic Disease (CMD) is the more established threat and does most of the damage. But scientists are even more alarmed by an outbreak of Cassava Brown Streak Disease (CBSD) - dubbed the "Ebola of plants."
      The disease is highly infectious, difficult to detect, and it mutates rapidly into new strains. Farmers often discover the tell-tale brown streaks only after their entire crop has been destroyed.
      The outbreak could have a catastrophic impact if it continues to spread. But local specialists are working with an international coalition and state-of-the-art technology to defeat it.
      Tell-tale signs of Cassava Brown Streak Disease (CBSD).

      Mapping disease

      Great swathes of Tanzanian farmland have been wiped out by CBSD.
      "We are seeing very severe food shortages," says Dr. Joseph Ndunguru, a plant virologist based in the East African state with the Cassava Diagnostics Project (CDP). "Farmers are just abandoning their crop, and in some areas cassava is the only staple food."
      The CDP is working in seven countries in East and Central Africa, educating farmers and local government about the problem, studying the spread of disease, and developing resistant varieties of cassava.
      "We generate maps to show the distribution of virus strains in all of the project countries," says Ndunguru. "We use them to decide where to deploy clean plant material."
      CDP teams test crops by trial and error. A variety of plant that thrives in one disease-prone area might die off in another where a different strain of the virus has taken hold. Ndunguru prefers to test his plants in the worst hotspots, plagued by multiple strains, to prove their durability. He is beginning to see encouraging results.
      "We have delivered clean planting material to farmers in areas where they were getting yields of five tons per hectare, and now they are getting 40 tons per hectare," he says proudly. "This is a huge increase that allows them to pay for healthcare and education."
      Dr. Joseph Ndunguru (center) in Malawi with colleagues working to identify and control cassava disease.

      Cracking the code

      The fight against cassava disease is making use of a potent new weapon: genomics.
      The CDP is a highly cosmopolitan venture, with funding from the Bill and Melinda Gates Foundation, and partners in academic institutions around the world. One valuable ally is a research group at the University of Western Australia (UWA) -- home to one of the world's most powerful supercomputers.
      The group performs advanced analysis on diseased plant samples from African farms that is currently impossible in the region.
      "These plants look sick but we don't know which virus is making them sick," says Dr. Laura Boykin, a computational biologist at UWA. "We do diagnostic tests looking for whole genomes (the complete set of DNA or RNA) of viruses, and to get them we have to study billions of base pairs."
      The practice is particularly useful with CBSD that spreads and mutates rapidly -- Boykin calls it "the Ebola of plants" - and has allowed the UWA team to discover new strains of the virus. The disease had been largely contained since it was discovered in the 1930s, until aggressive new strains emerged over the past decade.
      But transporting samples from East Africa to Australia for testing wastes valuable time. Diagnostic tools are needed in the field.
      This frustration is now being addressed through a partnership with UK sequencing special