doi:10.1038/nindia.2014.68 Published online 23 May 2014

Geographic hotspots where novel viruses could evolve

Shreya Dasgupta

Healthy cardamon plants (back) and infected dwarfed ones (front).

The aromatic spice large cardamom, a major cash crop grown only in parts of north-east India, Bhutan and Nepal, is seeing bad days – its yield has shrunk to less than half in the last ten years. A killer microbe – the cardamom bushy dwarf virus (CBDV) transmitted by aphids – has been ruining crops, much to the woe of farmers in the region.

Scientists now offer some hope in arresting this viral scourge – they say it is possible to identify geographic hotspots where such viruses could become more infective1.

Fiona Savory and colleagues from the National Centre for Biological Sciences in Bangalore assessed the genetic diversity of CBDV. Higher the genetic diversity, greater is the chance that new combinations of the virus might emerge, they say. This could make the virus more virulent or increase the spread of the disease.

CBDV belongs to a family of viruses with a peculiar multipartite genome found only in few plant viruses. The viral DNA is split into components, each encapsulated in a separate coating and playing a specific role in the life cycle. So when different viruses infect the same plant, their components can get shuffled to create newer viral strains, a process called reassortment. This reassortment generates genetic diversity in such viruses.

To pinpoint places where more novel and infective viruses can emerge, the team tried to identify locations where reassortment was most likely to occur. They collected leaf samples from 163 infected cardamom plants in Sikkim and parts of Darjeeling. From these samples, they isolated, amplified and sequenced the viral DNA, and built phylogenetic trees – trees depicting how the viruses are related.

“If two viruses that infect the same plant are closely related, reassortment will be limited. The offsprings will be pretty much like the parents,” says Savory. “But if you have genome components from distantly-related viruses reassembled together, you might get some novel genotypes.”

Fiona Savory (left) and colleagues collecting cardamom leaf samples and aphids.

Based on DNA analysis, the team identified two distinct populations of the virus. They also found two hotspots where reassortment was the greatest. One hotspot lies south of Gangtok in East Sikkim, where the two populations seem to collide forming a mixed population. “If you get the two populations co-infecting plants, you’ll have a problem,” says Savory. The second hotspot is in West Sikkim, close to Peling. Here, virus genotypes from a different population seem to have been introduced into the area, either by migratory aphids or by humans.

“As far as we know, this is one of the most extensive spatial sampling for plant viruses at finer scales," says Uma Ramakrishnan, a co-author of the study. “Very few people have thought of reassortment in a spatial context.”

Jer ming Hu of the National Taiwan University has worked on another multipartite plant virus. He is cautious about these conclusions. “The idea to identify virus reassortment hotspots is great, but could be controversial mostly due to erroneous sampling that could mislead the conclusion.”

Savory and team now plan to analyse the environmental factors that could predict disease prevalence in the region.

[Pictures courtesy: Fiona Savory]


1. Savory, F. R. et al. Identifying geographic hot spots of reassortment in a multipartite plant virus. Evol. Appl. (2014) doi: 10.1111/eva.12156