Barriers to gene flow between emerging populations of Watermelon mosaic virus in Southeastern France

Distribution and evolution of the major viruses infecting cucurbitaceous and solanaceous crops in the French Mediterranean area

Plant viral diseases represent a significant burden to plant health, and their highest impact in Mediterranean agriculture is on vegetables grown under intensive horticultural practices. In order to understand better virus evolution and emergence, the most prevalent viruses were mapped in the main cucurbitaceous (melon, squashes) and solanaceous (tomato, pepper) crops and in some wild hosts in the French Mediterranean area, and virus diversity, evolution and population structure were studied through molecular epidemiology approaches. Surveys were performed in summer 2016 and 2017, representing a total of 1530 crop samples and 280 weed samples. The plant samples were analysed using serological and molecular approaches, including high-throughput sequencing (HTS). The viral species and their frequency in crops were quite similar to those of surveys conducted ten years before in the same areas. Contrary to other Mediterranean countries, aphid-transmitted viruses remain the most prevalent in France whereas whitefly-transmitted ones have not yet emerged. However, HTS analysis of viral evolution revealed the appearance of undescribed viral variants, especially for watermelon mosaic virus (WMV) in cucurbits, or variants not present in France before, as for cucumber mosaic virus (CMV) in solanaceous crops. Deep sequencing also revealed complex virus populations within individual plants with frequent recombination or reassortment. The spatial genetic structure of cucurbit aphid-borne yellows virus (CABYV) was related to the landscape structure, whereas in the case of WMV, the recurrence of introduction events and probable human exchanges of plant material resulted in complex spatial pattern of genetic variation.

Genetic variability of watermelon mosaic virus isolates infecting cucurbit crops in Italy

Watermelon mosaic virus (WMV; genus Potyvirus, family Potyviridae) is responsible for serious cucurbit yield losses worldwide. Different WMV genetic groups have been characterized so far. Among these, the "classical" (CL) group has been present in the Mediterranean basin for 40 years, whereas the "emergent" (EM) group includes isolates that are associated with more-severe symptoms observed since 2000. Information on the spatial and temporal evolution of WMV isolates in Italy is currently sparse. In this study, 39 WMV isolates samples collected in different regions over the last two decades were analysed at two different genomic regions that are known to be highly variable and contain recombination breakpoints. Most of the isolates collected between 2002 and 2009 were found to belong to the CL group, whereas the isolates from 2012 onwards were classified as EM, indicating that EM isolates have progressively displaced the CL population in Italy. Although genetic variability was observed within both CL and EM groups and recombinant isolates were detected, no positive selection or haplotype geographic structure were inferred. This suggest that the shift from CL to EM populations was likely due to multiple introductions of EM isolates in different regions of Italy rather than from genetic differentiation of local populations. The progressive increase in prevalence of the highly virulent EM populations is a serious concern because of their symptom severity, and the presence of multiple EM variants that include recombinants necessitates new efforts to develop durable control strategies.

Pathogens in space: Advancing understanding of pathogen dynamics and disease ecology through landscape genetics

Landscape genetics has provided many insights into how heterogeneous landscape features drive processes influencing spatial genetic variation in free-living organisms. This rapidly developing field has focused heavily on vertebrates, and expansion of this scope to the study of infectious diseases holds great potential for landscape geneticists and disease ecologists alike. The potential application of landscape genetics to infectious agents has garnered attention at formative stages in the development of landscape genetics, but systematic examination is lacking. We comprehensively review how landscape genetics is being used to better understand pathogen dynamics. We characterize the field and evaluate the types of questions addressed, approaches used and systems studied. We also review the now established landscape genetic methods and their realized and potential applications to disease ecology. Lastly, we identify emerging frontiers in the landscape genetic study of infectious agents, including recent phylogeographic approaches and frameworks for studying complex multihost and host-vector systems. Our review emphasizes the expanding utility of landscape genetic methods available for elucidating key pathogen dynamics (particularly transmission and spread) and also how landscape genetic studies of pathogens can provide insight into host population dynamics. Through this review, we convey how increasing awareness of the complementarity of landscape genetics and disease ecology among practitioners of each field promises to drive important cross-disciplinary advances.

Exploiting Genetic Information to Trace Plant Virus Dispersal in Landscapes

During the past decade, knowledge of pathogen life history has greatly benefited from the advent and development of molecular epidemiology. This branch of epidemiology uses information on pathogen variation at the molecular level to gain insights into a pathogen's niche and evolution and to characterize pathogen dispersal within and between host populations. Here, we review molecular epidemiology approaches that have been developed to trace plant virus dispersal in landscapes. In particular, we highlight how virus molecular epidemiology, nourished with powerful sequencing technologies, can provide novel insights at the crossroads between the blooming fields of landscape genetics, phylogeography, and evolutionary epidemiology. We present existing approaches and their limitations and contributions to the understanding of plant virus epidemiology.

Molecular genetic analysis of cucumber mosaic virus populations infecting pepper suggests unique patterns of evolution in Korea

Studying genetic structure and diversity of viruses is important to understand the evolutionary mechanisms that generate and maintain variations in viral populations. Cucumber mosaic virus (CMV) is endemic in most pepper fields in Korea. Currently, no effective methods for control of CMV are available due to many environmental and biological factors such as the extensive evolutionary capacity of CMV. Thus, analyzing the genetic structure of CMV populations may facilitate the development of strategies for the control of CMV. In this study, 252 pepper (Capsicum annuum) samples showing virus symptoms were collected by field surveys performed throughout Korea in 2007. Reverse-transcription polymerase chain reaction analyses revealed that, in total, 165 collected samples were infected with CMV. Forty-five CMV isolates were randomly selected within each regional subpopulation and analyzed by full-genome sequencing. Analyses of genetic diversity showed that the 2b gene of CMV is under weaker purifying selection than the other genes. Based on the phylogenetic analysis of RNA1, the CMV isolates from pepper were divided into three clusters in subgroup I. Our full-genome sequence-based molecular analyses of the CMV Korean population suggest that the subpopulations of CMV have been geographically localized in pepper fields in Korea.

A short motif in the N-terminal part of the coat protein is a host-specific determinant of systemic infectivity for two potyviruses

Although the biological variability of Watermelon mosaic virus is limited, isolates from the three main molecular groups differ in their ability to infect systemically Chenopodium quinoa. Mutations were introduced in a motif of three or five amino acids located in the N-terminal part of the coat protein, and differing in isolates from group 1 (motif: lysine-glutamic acid-alanine (Lys-Glu-Ala) or KEA, systemic on C. quinoa), group 2 (Lys-Glu-Thr or KET, not systemic on C. quinoa) and group 3 (KEKET, not systemic on C. quinoa). Mutagenesis of KEKET in an isolate from group 3 to KEA or KEKEA was sufficient to make the virus systemic on C. quinoa, whereas mutagenesis to KET had no effect. Introduction of a KEA motif in Zucchini yellow mosaic virus coat protein also resulted in systemic infection on C. quinoa. These mutations had no obvious effect on the disorder profile or potential post-translational modifications of the coat protein as determined in silico.

Genetic variation of the Turnip mosaic virus population of Vietnam: a case study of founder, regional and local influences

Turnip mosaic virus (TuMV) is one of the most important viruses infecting a wide range of plant species, primarily from the family Brassicaceae. Thirty TuMV isolates were collected from Brassica and Raphanus plants in Vietnam during 2006-2008. Host reaction studies showed that many of the isolates belonged to Brassica/Raphanus (BR) host-infecting type. Sequence-based phylogenetic and population genetic analyses were made of the complete polyprotein gene sequences, and of four non-recombinogenic regions of those sequences (i.e. genes of the helper-component proteinase protein, protein 3, nuclear inclusion b protein and coat protein). These were used to assess the subpopulation differentiation and divergence between Vietnamese TuMV populations and those of nearby Asian countries. Nine inter- and intralineage recombination type patterns were identified in the genomes of the Vietnamese isolates, of which seven were novel. All the Vietnamese non-recombinant isolates fell into the world-B group of TuMV and clustered with Chinese isolates. The estimates of genetic differentiation and gene flow reveal that the TuMV populations of Vietnam, China and Japan are genetically linked but have clear local founder effects. This, the first population genetic study of a TuMV population in Southeast Asia, indicates the importance of such studies for providing the scientific basis of control strategies.

Viruses of cucurbit crops in the Mediterranean region: an ever-changing picture

Cucurbit crops may be affected by at least 28 different viruses in the Mediterranean basin. Some of these viruses are widely distributed and cause severe yield losses while others are restricted to limited areas or specific crops, and have only a negligible economic impact. A striking feature of cucurbit viruses in the Mediterranean basin is their always increasing diversity. Indeed, new viruses are regularly isolated and over the past 35 years one "new" cucurbit virus has been reported on average every 2 years. Among these "new" viruses some were already reported in other parts of the world, but others such as Zucchini yellow mosaic virus (ZYMV), one of the most severe cucurbit viruses and Cucurbit aphid-borne yellows virus (CABYV), one of the most prevalent cucurbit viruses, were first described in the Mediterranean area. Why this region may be a potential "hot-spot" for cucurbit virus diversity is not fully known. This could be related to the diversity of cropping practices, of cultivar types but also to the important commercial exchanges that always prevailed in this part of the world. This chapter describes the major cucurbit viruses occurring in the Mediterranean basin, discusses factors involved in their emergence and presents options for developing sustainable control strategies.

Cucumber mosaic virus

Cucumber mosaic virus (CMV) is an important virus because of its agricultural impact in the Mediterranean Basin and worldwide, and also as a model for understanding plant-virus interactions. This review focuses on those areas where most progress has been made over the past decade in our understanding of CMV. Clearly, a deep understanding of the role of the recently described CMV 2b gene in suppression of host RNA silencing and viral virulence is the most important discovery. These findings have had an impact well beyond the virus itself, as the 2b gene is an important tool in the studies of eukaryotic gene regulation. Protein 2b was shown to be involved in most of the steps of the virus cycle and to interfere with several basal host defenses. Progress has also been made concerning the mechanisms of virus replication and movement. However, only a few host proteins that interact with viral proteins have been identified, making this an area of research where major efforts are still needed. Another area where major advances have been made is CMV population genetics, where contrasting results were obtained. On the one hand, CMV was shown to be prone to recombination and to show high genetic diversity based on sequence data of different isolates. On the other hand, populations did not exhibit high genetic variability either within plants, or even in a field and the nearby wild plants. The situation was partially clarified with the finding that severe bottlenecks occur during both virus movement within a plant and transmission between plants. Finally, novel studies were undertaken to elucidate mechanisms leading to selection in virus population, according to the host or its environment, opening a new research area in plant-virus coevolution.

Search for factors involved in the rapid shift in Watermelon mosaic virus (WMV) populations in South-eastern France

Watermelon mosaic virus (WMV, genus Potyvirus, family Potyviridae) was reported for the first time in France in 1974, and it is now the most prevalent virus in cucurbit crops. In 2000, new strains referred as 'emerging' (EM) strains were detected in South-eastern France. EM strains are generally more severe and phylogenetically distinct from those previously reported in this country and referred as 'classic' (CL) strains. Since 2000, EM strains have been progressively replacing CL strains in several areas where they co-exist. In order to explain this rapid shift in virus populations, the biological properties of a set of 17 CL and EM WMV isolates were compared. No major differences were observed when comparing a limited host range including 48 different plant species or cultivars. Only two species were differential; Chenopodium quinoa was systemically infected by CL and not by EM isolates whereas Ranunculus sardous was systemically infected by EM and not by CL isolates. A considerable variability was observed in aphid transmission efficiencies but this could not be correlated to the CL or EM types. Two subsets of five isolates of each group were used to compare aphid transmission efficiencies from single and double (CL-EM) infections using six different cucurbit and non-cucurbit hosts. EM isolates were generally better transmitted from mixed CL-EM infections than CL isolates and CL transmission rates were significantly lower from double than from single infections. Cross-protection was only partial between CL and EM strains leading to frequent double infections, and only a slight asymmetry was observed in cross-protection efficiencies. Since double infections occur very commonly in fields, the preferential transmission of EM from mixed CL-EM infections could be one of the factors leading to the displacement of CL isolates by EM isolates.

Recombination in natural populations of watermelon mosaic virus: new agronomic threat or damp squib?

Since their introduction in south-eastern France around 1999, new, 'emerging' (EM) strains of watermelon mosaic virus (WMV) coexist with the 'classic' (CL) strains present for more than 40 years. This situation constitutes a unique opportunity to estimate the frequency of recombinants appearing in the few years following introduction of new strains of a plant RNA virus. Molecular analyses performed on more than 1000 isolates from epidemiological surveys (2004-2008) and from experimental plots (2009-2010), and targeting only recombinants that became predominant in at least one plant, revealed at least seven independent CL/EM or EM/EM recombination events. The frequency of recombinants involving at least one EM parent in the natural populations tested was on the order of 1 %. No new recombinant was detected for more than 1 year, and none but one in more than one location. In tests comparing host range and aphid transmissibility, the new recombinants did not display a better fitness than their 'parental' isolates. No recombinant was detected from artificial mixed infections of CL and EM isolates of various hosts after testing more than 1500 subcultures obtained after single-aphid transmission. These results constitute one of the first estimations of the frequency of recombinants in natural conditions for a plant RNA virus. This suggests that although viable recombinants of WMV are not rare, and although recombination may potentially lead to new highly damaging strains, the new recombinants observed so far had a lower fitness than the parental strains and did not emerge durably in the populations.