Solving an old problem with older data

Reddening under the bright Egyptian sun, British plant evolution specialist Robin Allaby sifted through desiccated soil. He was looking for seeds, and not just any seeds. These were peppered in the parched layers of the Nubian desert, near a remote town in southeast Egypt. They were almond-shaped, wheatish in color — imperfect specimens, certainly, but remarkably well preserved. They were deposited centuries ago, and were now uncovered with their delicate cellular structures still intact.

In one of these samples, dating back 750 years, Allaby and his team from the University of Warwick in the United Kingdom found the genetic material of the one of the major pathogens affecting modern agriculture, the barley stripe mosaic virus (BSMV). Allaby was surprised, because the virus was thought to be only 150 years old. When his team added this unique genetic data to that of specimens they had already collected, their models revealed a riveting new picture: the virus probably evolved 2,000 years ago, then spread across the world. Allaby’s team speculates that this may have been because of human movements during the Christian crusades of the Middle Ages, although other researchers have yet to corroborate this theory.

Plant pathogens like BSMV are one of the biggest threats to modern food security, the complex issue of ensuring consistent, accessible, healthy and nutritious sustenance. As global population explodes, diseases that decrease crop yields pose a serious threat to the already-strained global food supply. A more complete understanding of these plant viruses can show scientists how pathogens develop and spread — and perhaps that they began to spread far earlier than anyone anticipated. There can be a large number of other viruses out there that are affecting productivity that look like they are recent introductions but really aren’t, Allaby says; the virus’ age totally changes the picture of the modern pathogen landscape. If some viruses appear younger due to limited data, policy-makers might think that the transmission followed modern trade routes instead of more ancient dispersion methods. “Maybe it’s not the modern trade routes that are the things that need policing,” he adds.

When Allaby’s infected seed fell to the ground 750 years ago, barley was a staple crop in Egypt.  The virus that affected these plants, the barley stripe mosaic virus, infects 90 to 100 percent of the seeds it comes into contact with, stunting the plant’s growth and drastically reducing crop yields. Many of the thousands of samples that Allaby’s team unearthed from the parched strata were infected with the virus. Although many of the specimens had parts of the virus’ genetic code, Allaby’s sample was special. The region’s dry climate preserved almost all of its genetic information in the form of RNA, a nucleic acid like DNA that contains an organism’s instructions for how to make basic proteins. “RNA hasn’t had a lot of attention in the past,” Allaby says, because it tends to break down much more quickly than DNA. But because of the region’s especially dry climate, the RNA has broken down much slower than it typically does in more humid areas. In fact, it’s an impressive feat that Allaby and his team were able to sequence such an old specimen. “To have an RNA molecule that has persisted for so long is really cool,” says Olivia Wilkins, a post-doctoral fellow at the Center for Genomics and Systems Biology at New York University who studies plant genetics.

By comparing this ancient genetic sequence to that of more recent samples, the researchers were able to develop an algorithm to estimate the age of the virus. In the study, published recently in the journal Scientific Reports, the authors noted that previous estimates that calculated the virus to be 150 years old were based on data that was far too limited. The genetic data was only drawn from specimens within the past century, and, based on those minor genetic changes in the virus, BSMV seemed to be a young virus that had dispersed only recently. But this picture, formed by only a small amount of data, was incomplete — and misleading for those who research plant viruses. “By having an archaeological virus, an old calibration date appears… and an interesting story emerges,” Allaby says. “It massively changes your understanding of the origin of the virus.”

In fact, Allaby and his team theorized that the virus’ transmission around the globe could stem from a complex series of dispersions that may line up temporally with the Crusades, a series of military campaigns initiated by the Catholic Church that spanned two centuries of the Middle Ages. In the paper, Allaby’s team estimates the exact year of BSMV’s origin to be 1234, which “corresponds closely” to the Seventh Crusade that landed in Egypt. The infected seeds, Allaby believes, were then transported back to Europe and could have reached East Asia through transit on the Silk Road by the late medieval era (around 1500). But this research is still very preliminary. According to Christopher Tyerman, a medieval historian at Hertford College in the United Kingdom, “Associating [the] transmission of anything, including a virus, to a specific incident of contact is fraught with methodological problems and improbabilities.”

Although their origins may still be contested, the proliferation of plant diseases is a problem that governments must address on a global scale. Plant viruses account for half of the infectious diseases that threaten global food security. They cause discolorations, physical deformations and distorted leaves, leading to smaller and less nutritious crops, possibly even compromising public health. Amidst skyrocketing populations, countries around the world have started asking themselves: do we have enough to feed everyone? Countries that can today may not be able to by 2050, when the global population is estimated to reach a staggering 9.6 billion. With populations pushing these already-strained resources to the limit, governments are scrambling to maximize crop yields and safeguard existing assets.

Plant diseases are a pretty big and relevant issue to global food security, says Anna Applefield, a researcher with the Global Food Security Project based in Washington, D.C. Countries struggle to maintain a regulatory framework that allows for only safe trade with other countries — a feat that is particularly challenging in developing countries where government enforcement is not as efficient. But plant productivity is of the greatest concern, Applefield notes. While engineers labor furiously to increase crop yields, plant pathologists and politicians work to keep diseases — like BSMV — at bay.

“Plant diseases are transmitted in a number of different ways,” says NYU’s Wilkins. One such method is through insects — leafhopper insects, for example, are known to transmit 80 different viruses by jumping from plant to plant. Another common method is when an infected seed is put in contact with an uninfected seed. “In a non-cultivated system [as plants are in nature], you might end up with seed-to-seed contact just from neighboring plants blowing in the wind and seeds… touching one another,” Wilkins says. The barley virus can even hop between barley and other native grasses, which may have helped the virus spread, Allaby notes.

In an agricultural setting, most of the seeds are transported in large bags or even truckloads, so farmers end up with “a few infected seeds that get mixed in with uninfected seeds,” Wilkins says. “When they are planted in the field, the infected seeds may be distributed widely and so the infection may spread much more rapidly.” As BSMV spread across continents, infected seeds grew into mature barley plants that were shockingly small, and farmers could reap only paltry yields. It is this transport of infected seeds, Wilkins says, that trade regulators today try desperately to prevent in order to preserve their country’s crops.

“Through traditional and targeted breeding programs, researchers have bred plants that are outright resistant to a number of pathogens,” Wilkins says. At the International Rice Research Institute in the Philippines, biologists are breeding some types of naturally-occurring rice that are immune to rust, a fungal pathogen that stunts plant growth and diminishes yields. But efforts to engineer plants that are immune to viruses in particular have been less successful. Researchers have identified the genes to breed virus-resistant potatoes, but they have yet to breed a crop that is totally immune. In any event, Wilkins is skeptical that this is the right way to ensure food security. “Technology alone won’t end food shortages,” she says.

Despite an increasingly globalized world with easier travel between countries, most policymakers do not consider crop contamination inevitable, says Applefield. Regulators tend to be very conservative and restrict anything that may put domestic crops at risk, even in the light of promising data. As a result, the road to incorporating new virus information in international trade policy may be long and winding. “I think [Allaby’s study] has a lot of implications for how we think about viruses,” says Applefield. She imagines the same virus may have spread long ago between far-flung locations, but scientists just haven’t realized it yet. But the bar to change regulations is still very high. “Countries tend to be pretty protective of their [plant] populations,” she says. “I think, if a country wasn’t being affected as much by a disease, it would have to be convinced” to loosen its trade restrictions with countries that have more affected crops. And the best way to persuade policy-makers is with lots of data, much of which is simply not yet available.

Understanding how pathogens affect the world’s food supply continues to influence food security policy. “There’s a lot of stigma around viruses,” Applefield says. “A lot of effort and expense goes into trying to avoid them.” As scientists work to see the bigger picture in a virus’ history, policy-makers will work to apply this knowledge to the impending food shortage.

“When [resources] are in short supply, it really matters whether you’re making the most of them,” Wilkins says. Research like hers and Allaby’s may ensure that future populations are able to do so.