Molecular Ecology and Emergence of Tropical Plant Viruses

Abstract

An appreciation of the risks caused by emergent plant viruses is critical in tropical areas that rely heavily on agriculture for subsistence and rural livelihood. Molecular ecology, within 10 years, has unraveled the factors responsible for the emergence of several of the economically most important tropical plant viruses: Rice yellow mottle virus (RYMV), Cassava mosaic geminiviruses (CMGs), Maize streak virus (MSV), and Banana streak virus (BSV). A large range of mechanisms--most unsuspected until recently--were involved: recombination and synergism between virus species, new vector biotypes, genome integration of the virus, host adaptation, and long-distance dispersal. A complex chain of molecular and ecological events resulted in novel virus-vector-plant-environment interactions that led to virus emergence. It invariably involved a major agricultural change: crop introduction, cultural intensification, germplasm movement, and new genotypes. A current challenge is now to complement the analysis of the causes by an assessment of the risks of emergence. Recent attempts to assess the risks of emergence of virulent virus strains are described.

Incidence of viruses and virus-like diseases of watermelons and pumpkins in Uganda, a hitherto none-investigated pathosystem

“…Besides involvement of vectors, differences in virus incidences may reflect regional differences in the abundance of susceptible vs. resistant host genotypes grown by farmers, and variabilities in environmental parameters influencing virus transmission and disease development (Fargette et al, 2006;Geering and Randles, 2012). Accordingly, virus infection and symptom development in plants is a function of variable factors of environment, virus strain, host plant species or genotype, age, and the host's physiological state (Cooper and Jones, 2006).…”

“…However, the impact of plant virus diseases is exacerbated in the tropics because tropical conditions favour continuous presence of both primary and secondary hosts and super-abundance of vectors that efficiently transmit the viruses (Fargette et al, 2006;Morales, 2007;Barult et al, 2010;NavasCastillo et al, 2011;Geering and Randles, 2012;Fereres and Raccah, 2015). Moreover, virus diseases in nonpriority crops at local or regional scale when ignored or left to 'fallow' may constitute none investigated pathosystems as sources of harmful viruses in surrounding cropping systems (Jones et al, 2010;Lebeda and Burdon, 2013).…”

Questions and Concepts in Plant Virus Evolution: a Historical Perspective

“…Genetic exchange by recombination or reassortment of genomic segments (i.e., sexuality) is another important source of genetic variation in vimses, often with large phenotypic effects such as host switches, host range expansion and is often at the root of the emergency of new viral diseases. A typical example is the role of genetic exchange in the origin of the pandemic of cassava mosaic disease in East Africa (Fargette et al 2006), Genetic exchange also has been shown to be important in the evolution of taxonomic entities (White et al 1995). Genotypes generated by recombination can be frequent in virus populations, as shown particularly for begomoviruses (Sanz et al 2000), but also for RNA virus such as Turnip mosaic virus (TuMV) (Tan et al 2004).…”

“…Thus, there is a need to analyze virus evolution within broader epidemiologic al and ecological frames. Good examples of integration of ecological and epideliological data in virus evolution studies are in a series of reports on the volutionary biology of Rice yellow mottle virus (Fargette et al 2006) andTuMV Tomitaka andOhshima 2006). An important motor of research on virus evolution :om an ecological perspective is related to the development of transgenic plants nth pathogen-derived resistance, and the need to evaluate the risks that their widepread use could have for agricultural and wild ecosystems (Tepfer 2002).…”

A proposal to rationalize within-species plant virus nomenclature: benefits and implications of inaction

“…In contrast, employing partial genome sequences for phylogenetic analysis can produce misleading phylogenetic trees, which, when recombination occurs, often result in incorrect deductions about the positioning of isolates in within-species phylogenetic groups [18][19][20]29]. Other factors increasingly impacting on the sequences that make up within-species phylogenetic groups include emergence of known and novel viruses in new hosts or world regions driven by (i) new encounters between wild and crop plants at interfaces between wild and managed vegetation, (ii) rapidly expanding world trade in plants and plant products moving viruses and vectors around the world, (iii) agricultural intensification, extensification and diversification underway to feed the burgeoning world population, (iv) encroaching urbanization as population centers expand, and (v) climate change causing plant viruses to adapt, shift hosts and change their geographical distributions [1,3,4,7,[10][11][12][13][14]24].…”