Taking virus detection out of labs and into farmer fields in Africa

Deciphering viruses

Whereas human immune systems create antibodies to destroy viruses, plants have simpler defense responses that chop up a virus’s genetic material — ribonucleic acid (RNA) — when it enters a cell, hindering its ability to cause damage. In crops like sweet potato, viruses accumulate and pass from one generation to the next in planting material, diminishing the yield of each successive harvest. In regions of Africa where the whiteflies and aphids that spread sweetpotato viruses abound, transmission by planting material exacerbates the damage caused.

CIP virologist Jan Kreuze pioneered the use of genetic sequencing and reassembly of the RNA fragments from a plant’s anti-viral response to identify the sweetpotato viruses that infect it. Kreuze led a field study that analyzed tissue samples from 1,168 sweet potato plants in farmer fields across 11 African countries, identifying more than 15 viruses, some previously unknown.

The team then used the data to develop models to predict where specific viruses are likely to be found and how climate change will affect their distribution. Using a technology known as a LAMP assay, they identified genetic markers to develop a diagnostic field test for three common sweet potato viruses. The assay is vital because infected plants are often asymptomatic — as are many people with COVID-19 — which complicates detection.

In trials at four different sites in Kenya, the assay was 100 percent accurate, and both faster and cheaper than laboratory-based methods. Though delayed by COVID-19, scientists expect the tool to be available soon in Kenya, allowing for the removal of infected planting material from the seed system and the identification of virus-resistant varieties for farmers.

Diagnosis by phone

With the help of the assay, scientists are using photos of infected plants to develop artificial intelligence to enable the smartphone app Nuru (“Light” in Swahili) to provide farmers with a real-time diagnosis of sweetpotato virus infections via their phones. Developed by CGIAR and Penn State University scientists, the app is part of a platform called Plant Village that also provides instructions on managing pests and diseases. Nuru has been in use since 2018 to diagnose cassava and maize pests and diseases. Sweetpotato is one of a growing number of crops that it will provide diagnoses and advice for.

Both the app and LAMP assay are expected to help identify and control the most common viruses. But more work is needed to understand some previously unknown threats identified by Kreuze’s team. In field trials, scientists discovered that a group of common but asymptomatic viruses known as begomoviruses, which were assumed to be benign, reduced yields of a popular orange-fleshed sweetpotato variety by up to 40 percent.

“That this variety, which is resistant to the two most common sweet potato viruses, could suffer that much damage from a third, underlines how much we need to learn,” Kreuze said. “By improving farmer tools, increased crop yields will help put more nutritious food on the tables — and incomes in the pockets — of some of the world’s most vulnerable families.”