Population Genomics of Plant Viruses: The Ecology and Evolution of Virus Emergence

Abstract

The genomics era has revolutionized studies of adaptive evolution by monitoring large numbers of loci throughout the genomes of many individuals. Ideally, the investigation of emergence in plant viruses requires examining the population dynamics of both virus and host, their interactions with each other, with other organisms and the abiotic environment. Genetic mechanisms that affect demographic processes are now being studied with high-throughput technologies, traditional genetics methods, and new computational tools for big-data. In this review, we discuss the utility of these approaches to monitor and detect changes in virus populations within cells and individuals, and over wider areas across species and communities of ecosystems. The advent of genomics in virology has fostered a multi-disciplinary approach to tackling disease risk. The ability to make sense of the information now generated in this integrated setting is by far the most substantial obstacle to the ultimate goal of plant virology to minimize the threats to food security posed by disease. To achieve this goal, it is imperative to understand and forecast how populations respond to future changes in complex natural systems.

Molecular phylogenetics and evolutionary analysis of a highly recombinant begomovirus, Cotton leaf curl Multan virus, and associated satellites

“…2A ). Importantly, the observation of a commonly infected host or disease prevalence might be attributed to the possible effects of several factors like sampling biasness ( Lacroix et al 2016 ), virus–vector–host interactions, and the environmental heterogeneity among others ( McLeish, Fraile, and García-Arenal 2021 ). The host range of alphasatellites (CLCuMuA) from Pakistan and India varied greatly, although the most commonly infected host was observed to be cotton ( Fig.…”

Aphid‐borne viruses infecting cultivated watermelon and squash in Spain: Characterization of a variant of cucurbit aphid‐borne yellows virus (CABYV)

“…Heterogeneous host genotype populations (i.e., different host plants and varieties of cucurbits along with particular agroecological practices) may alter the epidemiological patterns of viral diseases (De Moya‐Ruiz et al, 2021; Juárez et al, 2019; Valverde et al, 2020). Hence, the systematic monitoring of the occurrence of viral diseases and their causative agents, combined with ecological and quantitative epidemiological approaches, is essential to understand and mitigate their consequences on crops and natural ecosystems (Jeger, 2020; McLeish et al, 2020). In addition, the genetic and biological characterization of the emerging viruses increases our understanding of the ecological epidemiology of the diseases and could facilitate their early detection and prompt action for their control.…”

Viruses Infecting Trees and Herbs That Produce Edible Fleshy Fruits with a Prominent Value in the Global Market: An Evolutionary Perspective

“…Aside from the molecular mechanisms governing the observed virus host range distribution, the number and diversity of virus families infecting EFFs offer a picture regarding the future emergence of novel viruses [26,27,[102][103][104][105][106][107]. For example, EFFs such as V. vinifera, Cucumis sp., Citrus sp., Capsicum sp., and Solanum sp., which showed to be infected by the highest number of virus families (Figure 4), could potentially promote virus encounters that might result in recombination and, thereby generate novel and emerging viral diseases.…”