About 70 percent of the world’s production of cocoa — chocolate’s main ingredient — comes from just six small countries of West Africa, where a blight disease that kills cacao trees is spreading rapidly, causing decline and death in some trees in less than one year after infection occurs. In its wake, the livelihood of farmers is at stake and rainforest is lost as growers expand their plantations to compensate for losses and avert a potential chocolate crisis. 

A University of Arizona scientist is trying to find answers to the potential chocolate crisis before it’s too late.

“There is almost no knowledge about who and where the enemy is — let alone what actions are needed to ensure the longevity of the crop in the region for the short and long terms,” says Judy Brown, a plant virologist at the UA’s College of Agriculture and Life Sciences who is working with African scientists and farmers to create greater awareness and develop ways to combat this disease. 

“The impact on farmers and their families in terms of health, food security and sociopolitical aspects is dire, and continues to be, as the rapid tree decline outbreak affects more and more trees.”

Little is known about the pathogen — especially its diversity — other than it being a virus that infects cacao plants and is transmitted by mealybugs, small insects that feed on the tree sap. Unlike most other major crops, which have been backed by a history of research to make them more productive, better adapted to environmental stresses and more resistant to disease, cacao essentially still is a wild plant largely neglected by research and improvement programs, including badly needed epidemiological studies to guide management, Brown says. 

“This has resulted in a situation that is like going to the doctor and being told, ‘Sorry, we have no way to test your blood, so we can’t tell you whether you ate something poisonous or you’re just lacking vitamins,'” she says. 

For more than 100 years, the “solution” has been to remove infected trees and replace them with healthy trees, according to Brown. This strategy is destined to fail in the long run, because by the time trees show symptoms, they have been infected for weeks or months, all the while spreading the virus to neighboring trees. 

The affected countries in West Africa are gearing up to remove infected trees, with more than 300,000 infected cacao trees being replaced in Côte d’Ivoire alone.

“This comes at an enormous expense, while research to understand the distribution of disease spread and to identify the specific sources of the viral pathogens has been minimal,” says Brown, underscoring the need to learn much more about the nature, origin and cause of the outbreaks.

Brown is determined to help change that. In collaboration with the U.S. Department of Agriculture’s Agricultural Research Service in Miami and Mars Inc., the candy company, her research group is developing molecular tools growers could use to spot infected cacao trees before they show symptoms. 

“First, we have to get a better idea of who the enemy is,” Brown says. To that end, her research group takes advantage of “deep genome sequencing,” a technology that seemed like science fiction just 20 years ago, when the technology was first developed to decipher the human genome. 

“We take leaf tissue samples from infected cacao trees and fish for genetic material,” she says. “This type of next-generation DNA sequencing is fairly new technology, and it allows us to look for unknown or undiscovered viruses in our samples.”  

Through a collaboration with researchers from Côte d’Ivoire, Ghana and Nigeria, Brown’s group obtained leaves from cacao plants showing swollen stems and different patterns of leaf and vein discolorations, the telltale signs of being affected by swollen shoot disease viruses. After just one round of deep sequencing, the researchers found that the virus that gave the disease its name — cacao swollen shoot disease — was in fact six or more different species, and they expect to discover more. 

“There is very little understanding of the genetic diversity of these viruses, or what that means in relation to how they interact with their host plants and their mealybug vectors,” Brown says. “It’s a complete black box.”

Of the previously unknown virus species, formerly known as cacao swollen shoot virus, or CSSV, one appears to be particularly deadly, according to a recent publication by Brown’s team. The cacao trees that it infects develop red blotches along the veins of its leaves, and they die within one to two years, before farmers can get even one crop out of them. 

Without molecular and bioinformatics tools and knowledge, those depending on cacao may succumb to pandemics, experts fear.  

“Their whole livelihood depends upon it,” Brown says. “If they have no income, they have no food, they have no clothes, no antibiotics, the kids don’t go to school. The same thing just happens in circles when people are weakened and live in poverty.

“The sequence data may sound esoteric but it is not, because it helps us understand a lot about the viruses and their epidemiology, much like the Centers for Disease Control does for HIV or Ebola. It helps with diagnostics so the growers know what they’re dealing with, as well as with long-term breeding efforts to help them make the best decisions to stave off the damage until a more permanent, knowledge-based solution is in hand.”