Abstract
Reassortment between different species or strains plays a key role in the evolution of multipartite plant viruses and can have important epidemiological implications. Identifying geographic locations where reassortant lineages are most likely to emerge could be a valuable strategy for informing disease management and surveillance efforts. We developed a predictive framework to identify potential geographic hot spots of reassortment based upon spatially explicit analyses of genome constellation diversity. To demonstrate the utility of this approach, we examined spatial variation in the potential for reassortment among Cardamom bushy dwarf virus (CBDV; Nanoviridae, Babuvirus) isolates in Northeast India. Using sequence data corresponding to six discrete genome components for 163 CBDV isolates, a quantitative measure of genome constellation diversity was obtained for locations across the sampling region. Two key areas were identified where viruses with highly distinct genome constellations cocirculate, and these locations were designated as possible geographic hot spots of reassortment, where novel reassortant lineages could emerge. Our study demonstrates that the potential for reassortment can be spatially dependent in multipartite plant viruses and highlights the use of evolutionary analyses to identify locations which could be actively managed to facilitate the prevention of outbreaks involving novel reassortant strains.
Highlights
Plant pathogens present a major challenge to food security and local economies as an estimated 10–16% of global food production is annually lost to disease (Strange and Scott 2005; Chakraborty and Newton 2011)
Genome constellation diversity Six discrete genome components were sequenced for 163 Cardamom bushy dwarf virus (CBDV) isolates collected throughout Sikkim and the Darjeeling district of West Bengal, Northeast India
Geographic overlap of isolates with distinct genome constellations To ascertain whether epidemiologically relevant reassortment events are likely to occur among CBDV isolates, we assessed whether isolates with distinct genome constellations cocirculate in the same geographic localities
Summary
Plant pathogens present a major challenge to food security and local economies as an estimated 10–16% of global food production is annually lost to disease (Strange and Scott 2005; Chakraborty and Newton 2011). Reassortment, or pseudo-recombination, occurs only in viruses with segmented genomes and involves the exchange of discrete genome components between different species or genetically distinct strains which coreplicate within the same host cell This process generates hybrid progeny with novel combinations of genome components inherited from different parental viruses and may lead to the emergence of highly virulent strains (Hou and Gilbertson 1996; Pita et al 2001; Gu et al 2007; Chakraborty et al 2008; Nelson et al 2008; Chen et al 2009) or facilitate adaptation to alternative hosts (Idris et al 2008; Ince et al 2013). Relevant research emphasis has focused almost exclusively on viruses with segmented genomes that are important in the context of global health, such as influenza viruses
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