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, slowing its ability to cause damage.

Kreuze pioneered the use of genetic sequencing and reassembly of RNA fragments from a plant’s anti-viral response to identify the sweetpotato viruses that infect it. He led a field study that analyzed tissue samples from 1,168 sweetpotato 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. They also identified genetic markers to develop a diagnostic field test for three common sweetpotato viruses using a technology known as a LAMP. The LAMP assay is vital because some infected plants are asymptomatic—like many people with COVID-19—which complicates detection.

The LAMP assay, which is faster and cheaper than laboratory-based methods, was tested at four different sites in Kenya and was 100% accurate. Though deployment was delayed by COVID-19, scientists expect the tool to be available soon in Kenya, allowing for the removal of infected planting material from seed systems and faster 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 the 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 used 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 they discovered that a group of common but asymptomatic viruses, known as begomoviruses, reduced yields of a popular orange-fleshed variety — widely considered virus resistant — by 40%.

“That this variety, which is resistant to the two most common sweetpotato viruses, could suffer that much damage from a third, underlines how much we need to learn,” Kreuze said.

“By better understanding viruses, and improving diagnostic tools, we can help increase crop yields,” he added. “This will put more nutritious food on the tables, and income in the pockets, of some of the world’s most vulnerable families.”