Future Scenarios for Plant Virus Pathogens as Climate Change Progresses

RHPS4 Targeted the G-Quadruplex of the 1a Gene of Cucumber Mosaic Virus to Inhibit Viral Proliferation

Small molecules targeting G-quadruplexes (G4s) in viruses could inhibit viral proliferation. The 1a protein of cucumber mosaic virus (CMV) act as RNA-dependent RNA polymerase (RdRp) that plays a crucial role in regulating the replication of CMV. In this study, four putative G4 sequences (CMV PQS1-PQS4) in the genetic coding region of CMV 1a were identified, and three of them (PQS2, PQS3, and PQS4) were confirmed to fold into G4 structures. The G4-ligand, RHPS4, could bind to CMV PQS2 and PQS4 with a strong binding affinity and preferred to interact with the 3' terminal G-quartet surfaces of CMV PQS2, and 5' terminal of CMV PQS4. RHPS4 was also found to stabilize the CMV PQS2 and PQS4 G4s. Further studies revealed that RHPS4 exhibited an excellent anti-CMV activity. This study suggested that CMV PQS2 and PQS4 could be considered potential targets for screening viral inhibitors.

Rice Yellow Mottle Virus (RYMV): A Review

Rice (Oryza spp.) is mostly grown directly from seed and sown on wet or dry seed beds or usually used as transplants on nursery beds. Among all the economically important viral diseases in the world, rice yellow mottle virus (RYMV) is only prevalent in rice-growing countries in Africa. RYMV has become the main rice production constraint in Africa over the last 20-25 years, causing yield losses of 10 to 100% depending on the age of the plant at the time of infection, degree of varietal susceptibility and the existing climatic conditions. Good agricultural practices and biotechnological tools in the development of improved resistant cultivars have been extensively utilized in controlling the disease. This review focuses on RYMV, its epidemiology, serological and molecular typing, disease management and the way forward for sustainable rice production.

Unusual outbreaks of curly top disease in processing tomato fields in northern California in 2021 and 2022 were caused by a rare strain of beet curly top virus and facilitated by extreme weather events

In the western United States, curly top disease (CTD) is caused by beet curly top virus (BCTV). In California, CTD causes economic loss to processing tomato production in central and southern areas but, historically, not in the north. Here, we document unusual CTD outbreaks in processing tomato fields in the northern production area in 2021 and 2022, and show that these were caused by the rare spinach curly top strain (BCTV-SpCT). These outbreaks were associated with proximity of fields to foothills and unusually hot, dry, and windy spring weather conditions, possibly by altering migrations of the beet leafhopper (BLH) vector from locations with BCTV-SpCT reservoirs. Support for this hypothesis came from the failure to observe CTD outbreaks and BLH migrations in 2023, when spring weather conditions were cool and wet. Our results show the climate-induced emergence of a rare plant virus strain to cause an economically important disease in a new crop and location.

Australian Cool-Season Pulse Seed-Borne Virus Research: 1. Alfalfa and Cucumber Mosaic Viruses and Less Important Viruses

Here, we review the research undertaken since the 1950s in Australia's grain cropping regions on seed-borne virus diseases of cool-season pulses caused by alfalfa mosaic virus (AMV) and cucumber mosaic virus (CMV). We present brief background information about the continent's pulse industry, virus epidemiology, management principles and future threats to virus disease management. We then take a historical approach towards all past investigations with these two seed-borne pulse viruses in the principal cool-season pulse crops grown: chickpea, faba bean, field pea, lentil, narrow-leafed lupin and white lupin. With each pathosystem, the main focus is on its biology, epidemiology and management, placing particular emphasis on describing field and glasshouse experimentation that enabled the development of effective phytosanitary, cultural and host resistance control strategies. Past Australian cool-season pulse investigations with AMV and CMV in the less commonly grown species (vetches, narbon bean, fenugreek, yellow and pearl lupin, grass pea and other Lathyrus species) and those with the five less important seed-borne pulse viruses also present (broad bean stain virus, broad bean true mosaic virus, broad bean wilt virus, cowpea mild mottle virus and peanut mottle virus) are also summarized. The need for future research is emphasized, and recommendations are made regarding what is required.

Discovery of novel phenothiazine derivatives as new agrochemical alternatives for treating plant viral diseases

BACKGROUND

Plant viral diseases, namely 'plant cancer', are extremely difficult to control. Even worse, few antiviral agents can effectively control and totally block viral infection. There is an urgent need to explore and discover novel agrochemicals with high activity and a unique mode of action to manage these refractory diseases.

RESULTS

Forty-one new phenothiazine derivatives were prepared and their inhibitory activity against tobacco mosaic virus (TMV) was assessed. Compound A8 had the highest protective activity against TMV, with a half-maximal effective concentration (EC50 ) of 115.67 μg/mL, which was significantly better than that of the positive controls ningnanmycin (271.28 μg/mL) and ribavirin (557.47 μg/mL). Biochemical assays demonstrated that compound A8 could inhibit TMV replication by disrupting TMV self-assembly, but also enabled the tobacco plant to enhance its defense potency by increasing the activities of various defense enzymes.

CONCLUSION

In this study, novel phenothiazine derivatives were elaborately fabricated and showed remarkable anti-TMV behavior that possessed the dual-action mechanisms of inhibiting TMV assembly and invoking the defense responses of tobacco plants. Moreover, new agrochemical alternatives based on phenothiazine were assessed for their antiviral activities and showed extended agricultural application. © 2023 Society of Chemical Industry.

Inhibition of pepper huasteco yellow veins virus by foliar application of ZnO nanoparticles in Capsicum annuum L

The Pepper huasteco yellow vein virus (PHYVV) is an endemic geminivirus in Mexico causing partial or total losses in the pepper crop since the damage caused by the virus has not been fully controlled. In this work, we evaluated the effect of ZnO NPs (0, 50, 100, 150, and 200 mM) as a preventive (72 h before) and curative (72 h after) treatment of PHYVV infection in two jalapeño pepper varieties. In this study, we observed a decrease in symptoms, and it could be caused by an induction of the defense system in pepper plants and a direct action on PHYVV by foliar application of ZnO NPs. Our findings suggest that ZnO NP application significantly decreased the viral titer for both varieties at 200 mM by 15.11-fold. However, this effect was different depending on the timing of application and the variety of pepper. The greatest decrease in the viral titer in the preventive treatment in both varieties was at the concentration of 200 mM (1781.17 and 274.5 times, respectively). For curative treatment in cv. Don Pancho at the concentration of 200 mM (333.33 times) and cv. Don Benito at 100 mM (43.10 folds). compared to control. Furthermore, virus mobility was generally restricted for both varieties at 100 mM (15.13-fold) compared to the control. The results possibly delineated that ZnO NPs increased plant resistance possibly by increasing POD (2.08 and 0.25 times) and SOD (0.998 and 1.38) in cv. Don Pancho and cv. Don Benito, respectively. On the other hand, in cv. Don Pancho and cv. Don Benito presented a decrease in CAT (0.61 and 0.058) and PAL (0.78 and 0.77), respectively. Taken together, we provide the first evidence to demonstrate the effect of ZnO NPs on viral symptoms depending on the plan-virus-ZnO NP interaction.

Environmental Conditions Modulate Plant Virus Vertical Transmission and Survival of Infected Seeds

Seed transmission is a major mode for plant virus persistence and dispersal, as it allows for virus survival within the seed in unfavorable conditions and facilitates spread when they become more favorable. To access these benefits, viruses require infected seeds to remain viable and germinate in altered environmental conditions, which may also be advantageous for the plant. However, how environmental conditions and virus infection affect seed viability, and whether these effects modulate seed transmission rate and plant fitness, is unknown. To address these questions, we utilized turnip mosaic virus, cucumber mosaic virus, and Arabidopsis thaliana as model systems. Using seeds from plants infected by these viruses, we analyzed seed germination rates, as a proxy of seed viability, and virus seed transmission rate under standard and altered temperature, CO2, and light intensity. With these data, we developed and parameterized a mathematical epidemiological model to explore the consequences of the observed alterations on virus prevalence and persistence. Altered conditions generally reduced overall seed viability and increased virus transmission rate compared with standard conditions, which indicated that under environmental stress, infected seeds are more viable. Hence, virus presence may be beneficial for the host. Subsequent simulations predicted that enhanced viability of infected seeds and higher virus transmission rate may increase virus prevalence and persistence in the host population under altered conditions. This work provides novel information on the influence of the environment in plant virus epidemics. [Formula: see text] Copyright © 2023 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.

Salicylic acid and jasmonic acid in elevated CO2-induced plant defense response to pathogens

Plants respond to elevated CO₂ (eCO₂) via a variety of signaling pathways that often rely on plant hormones. In particular, phytohormone salicylic acid (SA) and jasmonic acid (JA) play a key role in plant defense against diverse pathogens at eCO₂. eCO₂ affects the synthesis and signaling of SA and/or JA and variations in SA and JA signaling lead to variations in plant defense responses to pathogens. In general, eCO₂ promotes SA signaling and represses the JA pathway, and thus diseases caused by biotrophic and hemibiotrophic pathogens are typically suppressed, while the incidence and severity of diseases caused by necrotrophic fungal pathogens are enhanced under eCO₂ conditions. Moreover, eCO₂-induced modulation of antagonism between SA and JA leads to altered plant immunity to different pathogens. Notably, research in this area has often yielded contradictory findings and these responses vary depending on plant species, growth conditions, photoperiod, and fertilizer management. In this review, we focus on the recent advances in SA, and JA signaling pathways in plant defense and their involvement in plant immune responses to pathogens under eCO₂. Since atmospheric CO₂ will continue to increase, it is crucial to further explore how eCO₂ may alter plant defense and host-pathogen interactions in the context of climate change in both natural as well as agricultural ecosystems.

Genetic analysis of resistance to bean leaf crumple virus identifies a candidate LRR-RLK gene

Bean leaf crumple virus (BLCrV) is a novel begomovirus (family Geminiviridae, genus Begomovirus) infecting common bean (Phaseolus vulgaris L.), threatening bean production in Latin America. Genetic resistance is required to ensure yield stability and reduce the use of insecticides, yet the available resistance sources are limited. In this study, three common bean populations containing a total of 558 genotypes were evaluated in different yield and BLCrV resistance trials under natural infection in the field. A genome-wide association study identified the locus BLC7.1 on chromosome Pv07 at 3.31 Mbp, explaining 8 to 16% of the phenotypic variation for BLCrV resistance. In comparison, whole-genome regression models explained 51 to 78% of the variation and identified the same region on Pv07 to confer resistance. The most significantly associated markers were located within the gene model Phvul.007G040400, which encodes a leucine-rich repeat receptor-like kinase subfamily III member and is likely to be involved in the innate immune response against the virus. The allelic diversity within this gene revealed five different haplotype groups, one of which was significantly associated with BLCrV resistance. As the same genome region was previously reported to be associated with resistance against other geminiviruses affecting common bean, our study highlights the role of previous breeding efforts for virus resistance in the accumulation of positive alleles against newly emerging viruses. In addition, we provide novel diagnostic single-nucleotide polymorphism markers for marker-assisted selection to exploit BLC7.1 for breeding against geminivirus diseases in one of the most important food crops worldwide.

Translating virome analyses to support biosecurity, on-farm management, and crop breeding

Virome analysis via high-throughput sequencing (HTS) allows rapid and massive virus identification and diagnoses, expanding our focus from individual samples to the ecological distribution of viruses in agroecological landscapes. Decreases in sequencing costs combined with technological advances, such as automation and robotics, allow for efficient processing and analysis of numerous samples in plant disease clinics, tissue culture laboratories, and breeding programs. There are many opportunities for translating virome analysis to support plant health. For example, virome analysis can be employed in the development of biosecurity strategies and policies, including the implementation of virome risk assessments to support regulation and reduce the movement of infected plant material. A challenge is to identify which new viruses discovered through HTS require regulation and which can be allowed to move in germplasm and trade. On-farm management strategies can incorporate information from high-throughput surveillance, monitoring for new and known viruses across scales, to rapidly identify important agricultural viruses and understand their abundance and spread. Virome indexing programs can be used to generate clean germplasm and seed, crucial for the maintenance of seed system production and health, particularly in vegetatively propagated crops such as roots, tubers, and bananas. Virome analysis in breeding programs can provide insight into virus expression levels by generating relative abundance data, aiding in breeding cultivars resistant, or at least tolerant, to viruses. The integration of network analysis and machine learning techniques can facilitate designing and implementing management strategies, using novel forms of information to provide a scalable, replicable, and practical approach to developing management strategies for viromes. In the long run, these management strategies will be designed by generating sequence databases and building on the foundation of pre-existing knowledge about virus taxonomy, distribution, and host range. In conclusion, virome analysis will support the early adoption and implementation of integrated control strategies, impacting global markets, reducing the risk of introducing novel viruses, and limiting virus spread. The effective translation of virome analysis depends on capacity building to make benefits available globally.

Comparative profiling of volatile organic compounds associated to temperature sensitive resistance to wheat streak mosaic virus (WSMV) in resistant and susceptible wheat cultivars at normal and elevated temperatures

To investigate changes in wheat resistance to wheat streak mosaic virus (WSMV) at normal and elevated temperatures and their effects on the emission of volatile organic compounds (VOCs), the profile of these compounds in WSMV-resistant (R) and susceptible (S) wheat cultivars were analyzed. VOCs were discovered in leaves of R and S cultivars inoculated to WSMV at 20 °C and 32 °C at 24, 48 and 72 h post inoculation (hpi) by GC. MS-HS-SPME. Many VOCs and related metabolic pathways of WSMV inoculated and control plants responded differently at low/high temperatures in R/S cultivars. Compounds such as 6-methyl-5-hepten-2-one and heptanal, represented the maximum abundance in R plants compared to S plants at earlier times especially, 48 hpi/20 °C. Also, at 32 °C, VOCs including heptanal and 2-pentenal had the highest increase in abundance at a later time. In addition, in R plants, several pathways were up-regulated commonly at 20 °C and 32 °C. Although, at 20 °C, they were activated at an earlier time. At 32 °C, most of these pathways were up-regulated at 72 hpi. The most important pathways correlated to combined stresses included lipoxygenase, cuticular wax biosynthesis, fatty acid and lipid biosynthesis. The pathway of phenyl ethanol biosynthesis was up-regulated only at 32 °C, which probably is specifically related to resistance to heat stress. Up-regulation of the lipoxygenase pathway appears to increase vector attractiveness and tolerance to biotic and abiotic stresses. Based on these results, is suggested that there is a particular synchronized regulation of defense-related multi-dimensional VOCs emitting network that is necessary for the occurrence of wheat defense responses against WSMV and/or heat. This research highlights the challenge of global warming and the breakdown of plant resistance to viruses which requires metabolic engineering of VOCs for sustainable agriculture.

Genomic High Plains Wheat Mosaic Virus Sequences from Australia: Their Phylogenetics and Evidence for Emaravirus Recombination and Reassortment

High Plains wheat mosaic virus (HPWMoV) causes a serious disease in major wheat-growing regions worldwide. We report here the complete or partial genomic sequences of five HPWMoV isolates from Australian wheat samples. Phylogenetic analysis of the nucleotide sequences of the eight genomic segments of these five isolates together with others from Genbank found all eight genes formed two lineages, L1 and L2. L1 contained a single isolate from Colorado in the North American Great Plains Region (GPR), and L2 had two unresolved clusters, A and B, of isolates from Australia and the GPR. A quarter of the L2B isolate sequences of the nucleocapsid gene (RNA3) were recombinant, which is unexpected as little evidence of recombination exists in viruses with negative single-stranded RNA genomes. Phylogenies calculated from the amino acid sequences of HPWMoV's RNA-dependent RNA-polymerase (RNA1), glycoprotein (RNA2), and nucleocapsid protein (RNA3) showed they were closest to those of Palo Verde broom virus. However, its movement protein (RNA4) was closer to those of Ti ringspot-associated and common oak ringspot-associated viruses, indicating the RNA4 segments of their ancestors reassorted to produce the current emaraviruses. To avoid increased yield losses from co-infection, biosecurity measures are advised to avoid HPWMoV introduction to countries where wheat streak mosaic virus already occurs.

Challenges and opportunities for plant viruses under a climate change scenario

There is an increasing societal awareness on the enormous threat that climate change may pose for human, animal and plant welfare. Although direct effects due to exposure to heat, drought or elevated greenhouse gasses seem to be progressively more obvious, indirect effects remain debatable. A relevant aspect to be clarified relates to the relationship between altered environmental conditions and pathogen-induced diseases. In the particular case of plant viruses, it is still unclear whether climate change will primarily represent an opportunity for the emergence of new infections in previously uncolonized areas and hosts, or if it will mostly be a strong constrain reducing the impact of plant virus diseases and challenging the pathogen's adaptive capacity. This review focuses on current knowledge on the relationship between climate change and the outcome plant-virus interactions. We summarize work done on how this relationship modulates plant virus pathogenicity, between-host transmission (which include the triple interaction plant-virus-vector), ecology, evolution and management of the epidemics they cause. Considering these studies, we propose avenues for future research on this subject.

Determinants of Virus Variation, Evolution, and Host Adaptation

Virus evolution is the change in the genetic structure of a viral population over time and results in the emergence of new viral variants, strains, and species with novel biological properties, including adaptation to new hosts. There are host, vector, environmental, and viral factors that contribute to virus evolution. To achieve or fine tune compatibility and successfully establish infection, viruses adapt to a particular host species or to a group of species. However, some viruses are better able to adapt to diverse hosts, vectors, and environments. Viruses generate genetic diversity through mutation, reassortment, and recombination. Plant viruses are exposed to genetic drift and selection pressures by host and vector factors, and random variants or those with a competitive advantage are fixed in the population and mediate the emergence of new viral strains or species with novel biological properties. This process creates a footprint in the virus genome evident as the preferential accumulation of substitutions, insertions, or deletions in areas of the genome that function as determinants of host adaptation. Here, with respect to plant viruses, we review the current understanding of the sources of variation, the effect of selection, and its role in virus evolution and host adaptation.

Perspectives on plant virus diseases in a climate change scenario of elevated temperatures

Global food production is at risk from many abiotic and biotic stresses and can be affected by multiple stresses simultaneously. Virus diseases damage cultivated plants and decrease the marketable quality of produce. Importantly, the progression of virus diseases is strongly affected by changing climate conditions. Among climate-changing variables, temperature increase is viewed as an important factor that affects virus epidemics, which may in turn require more efficient disease management. In this review, we discuss the effect of elevated temperature on virus epidemics at both macro- and micro-climatic levels. This includes the temperature effects on virus spread both within and between host plants. Furthermore, we focus on the involvement of molecular mechanisms associated with temperature effects on plant defence to viruses in both susceptible and resistant plants. Considering various mechanisms proposed in different pathosystems, we also offer a view of the possible opportunities provided by RNA -based technologies for virus control at elevated temperatures. Recently, the potential of these technologies for topical field applications has been strengthened through a combination of genetically modified (GM)-free delivery nanoplatforms. This approach represents a promising and important climate-resilient substitute to conventional strategies for managing plant virus diseases under global warming scenarios. In this context, we discuss the knowledge gaps in the research of temperature effects on plant-virus interactions and limitations of RNA-based emerging technologies, which should be addressed in future studies.

Ecology of Yellow Dwarf Viruses in Crops and Grasslands: Interactions in the Context of Climate Change

Our understanding of the ecological interactions between plant viruses, their insect vectors, and their host plants has increased rapidly over the past decade. The suite of viruses known collectively as the yellow dwarf viruses infect an extensive range of cultivated and noncultivated grasses worldwide and is one of the best-studied plant virus systems. The yellow dwarf viruses are ubiquitous in cereal crops, where they can significantly limit yields, and there is growing recognition that they are also ubiquitous in grassland ecosystems, where they can influence community dynamics. Here, we discuss recent research that has explored (a) the extent and impact of yellow dwarf viruses in a diversity of plant communities, (b) the role of vector behavior in virus transmission, and (c) the prospects for impacts of climate change-including rising temperatures, drought, and elevated CO₂-on the epidemiology of yellow dwarf viruses.

Screening a collection of local and foreign varieties of Solanum lycopersicum L. in Kazakhstan for genetic markers of resistance against three tomato viruses

The tomato is one of the most important vegetable crops. The successful development of tomato cultures in Kazakhstan depends on the implementation of intensive agricultural methods, including breeding and selecting for new tomato varieties resistant to plant pathogens. Common tomato viruses, although not detected in our country to date, may potentially have a deleterious impact on agriculture if allowed to spread. The implementation of tomato breeding programs based on molecular markers of resistance is therefore an important preventive measure for protecting the agriculture and food safety of Kazakhstan. In the present work, we used nine molecular markers associated with resistance to three tomato viruses, i.e., tomato mosaic virus (ToMV), tomato spot wilt virus (TSWV), and tomato yellow leaf curl virus (TYLCV), to test the local breeding collection for the presence of genetic resistance factors. Two tomato varieties, 'Zhiraf' (Russia) and 'Sunnik' (Armenia), were revealed to possess the resistant allele marker PrRuG86-151 against ToMV; three hybrid forms had the same allele in the heterozygous state. One hybrid, based on the 'Mirsini' F1 variety from the Netherlands, had resistance to TSWV, which was confirmed by four markers: NCSw003, NCSw007, NCSw011, and NCSw012. Two cultivars, 'Nicola' and 'Malinovyi Slon' (Russia), and the local hybrid based on 'Yarkiy Rumyanets' had two to three resistant alleles of markers based on locus Tm-3 of resistance to TYLCV. The obtained results have demonstrated that the collection of tomato varieties involved in breeding programs in Kazakhstan lacks well-known genetic resistance factors to the considered tomato viruses. Thus, the prospective breeding programs require introduction of known resistant genetic resources to establish resistance to viruses using marker-assisted selection.

Thermal stress triggers productive viral infection of a key coral reef symbiont

Climate change-driven ocean warming is increasing the frequency and severity of bleaching events, in which corals appear whitened after losing their dinoflagellate endosymbionts (family Symbiodiniaceae). Viral infections of Symbiodiniaceae may contribute to some bleaching signs, but little empirical evidence exists to support this hypothesis. We present the first temporal analysis of a lineage of Symbiodiniaceae-infecting positive-sense single-stranded RNA viruses ("dinoRNAVs") in coral colonies, which were exposed to a 5-day heat treatment (+2.1 °C). A total of 124 dinoRNAV major capsid protein gene "aminotypes" (unique amino acid sequences) were detected from five colonies of two closely related Pocillopora-Cladocopium (coral-symbiont) combinations in the experiment; most dinoRNAV aminotypes were shared between the two coral-symbiont combinations (64%) and among multiple colonies (82%). Throughout the experiment, seventeen dinoRNAV aminotypes were found only in heat-treated fragments, and 22 aminotypes were detected at higher relative abundances in heat-treated fragments. DinoRNAVs in fragments of some colonies exhibited higher alpha diversity and dispersion under heat stress. Together, these findings provide the first empirical evidence that exposure to high temperatures triggers some dinoRNAVs to switch from a persistent to a productive infection mode within heat-stressed corals. Over extended time frames, we hypothesize that cumulative dinoRNAV production in the Pocillopora-Cladocopium system could affect colony symbiotic status, for example, by decreasing Symbiodiniaceae densities within corals. This study sets the stage for reef-scale investigations of dinoRNAV dynamics during bleaching events.

The "Regulator" Function of Viruses on Ecosystem Carbon Cycling in the Anthropocene

Viruses act as "regulators" of the global carbon cycle because they impact the material cycles and energy flows of food webs and the microbial loop. The average contribution of viruses to the Earth ecosystem carbon cycle is 8.6‰, of which its contribution to marine ecosystems (1.4‰) is less than its contribution to terrestrial (6.7‰) and freshwater (17.8‰) ecosystems. Over the past 2,000 years, anthropogenic activities and climate change have gradually altered the regulatory role of viruses in ecosystem carbon cycling processes. This has been particularly conspicuous over the past 200 years due to rapid industrialization and attendant population growth. The progressive acceleration of the spread and reproduction of viruses may subsequently accelerate the global C cycle.

Effects of Elevated Temperature on the Susceptibility of Capsicum Plants to Capsicum Chlorosis Virus Infection

Capsicum, an important vegetable crop in Queensland, Australia, is vulnerable to both elevated temperatures and capsicum chlorosis virus (CaCV). Thus, it is imperative to understand the genetic responses of capsicum plants (Capsicum annuum) to CaCV under elevated temperature conditions. Here, we challenged susceptible plants (cv. Yolo Wonder) with CaCV and investigated the effects of elevated temperature on symptom expression, the accumulation of virus-derived short interfering RNA (vsiRNA) and viral RNA, and the expression of plant defense-associated genes. CaCV-inoculated plants initially showed more severe symptoms and higher viral concentrations at a higher temperature (HT, 35 °C) than at ambient temperature (AT, 25 °C). However, symptom recovery and reduced viral RNA accumulation were seen in the CaCV-infected plants grown at HT at later stages of infection. We also observed that HT enhanced the accumulation of vsiRNAs and that, concurrently, RNA interference (RNAi)-related genes, including Dicer-like2 (DCL2), DCL4, RNA-dependent RNA polymerase 1 (RdRp1), RdRp6, and Argonaute2 (AGO2), were upregulated early during infection. Moreover, continuous high levels of vsiRNAs were observed during later stages of CaCV infection at HT. Overall, our investigation suggests that HT facilitates CaCV replication during early infection stages. However, this appears to lead to an early onset of antiviral RNA silencing, resulting in a subsequent recovery from CaCV in systemic leaves.

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

Trees and herbs that produce fruits represent the most valuable agricultural food commodities in the world. However, the yield of these crops is not fully achieved due to biotic factors such as bacteria, fungi, and viruses. Viruses are capable of causing alterations in plant growth and development, thereby impacting the yield of their hosts significantly. In this work, we first compiled the world's most comprehensive list of known edible fruits that fits our definition. Then, plant viruses infecting those trees and herbs that produce fruits with commercial importance in the global market were identified. The identified plant viruses belong to 30 families, most of them containing single-stranded RNA genomes. Importantly, we show the overall picture of the host range for some virus families following an evolutionary approach. Further, the current knowledge about plant-virus interactions, focusing on the main disorders they cause, as well as yield losses, is summarized. Additionally, since accurate diagnosis methods are of pivotal importance for viral diseases control, the current and emerging technologies for the detection of these plant pathogens are described. Finally, the most promising strategies employed to control viral diseases in the field are presented, focusing on solutions that are long-lasting.

Climate Change and Emerging Food Safety Issues: A Review

ABSTRACT

Throughout the past decades, climate change has been one of the most complex global issues. Characterized by worldwide alterations in weather patterns, along with a concomitant increase in the temperature of the Earth, climate change will undoubtedly have significant effects on food security and food safety. Climate change engenders climate variability: significant variations in weather variables and their frequency. Both climate variability and climate change are thought to threaten the safety of the food supply chain through different pathways. One such pathway is the ability to exacerbate foodborne diseases by influencing the occurrence, persistence, virulence and, in some cases, toxicity of certain groups of disease-causing microorganisms. Food safety can also be compromised by various chemical hazards, such as pesticides, mycotoxins, and heavy metals. With changes in weather patterns, such as lower rainfall, higher air temperature, and higher frequency of extreme weather events among others, this translates to emerging food safety concerns. These include the shortage of safe water for irrigation of agricultural produce, greater use of pesticides due to pest resistance, increased difficulty in achieving a well-controlled cold chain resulting in temperature abuse, or the occurrence of flash floods, which cause runoff of chemical contaminants in natural water courses. Together, these can result in foodborne infection, intoxication, antimicrobial resistance, and long-term bioaccumulation of chemicals and heavy metals in the human body. Furthermore, severe climate variability can result in extreme weather events and natural calamities, which directly or indirectly impair food safety. This review discusses the causes and impacts of climate change and variability on existing and emerging food safety risks and also considers mitigation and adaptation strategies to address the global warming and climate change problem.

HIGHLIGHTS

Virus Diseases of Cereal and Oilseed Crops in Australia: Current Position and Future Challenges

This review summarizes research on virus diseases of cereals and oilseeds in Australia since the 1950s. All viruses known to infect the diverse range of cereal and oilseed crops grown in the continent's temperate, Mediterranean, subtropical and tropical cropping regions are included. Viruses that occur commonly and have potential to cause the greatest seed yield and quality losses are described in detail, focusing on their biology, epidemiology and management. These are: barley yellow dwarf virus, cereal yellow dwarf virus and wheat streak mosaic virus in wheat, barley, oats, triticale and rye; Johnsongrass mosaic virus in sorghum, maize, sweet corn and pearl millet; turnip yellows virus and turnip mosaic virus in canola and Indian mustard; tobacco streak virus in sunflower; and cotton bunchy top virus in cotton. The currently less important viruses covered number nine infecting nine cereal crops and 14 infecting eight oilseed crops (none recorded for rice or linseed). Brief background information on the scope of the Australian cereal and oilseed industries, virus epidemiology and management and yield loss quantification is provided. Major future threats to managing virus diseases effectively include damaging viruses and virus vector species spreading from elsewhere, the increasing spectrum of insecticide resistance in insect and mite vectors, resistance-breaking virus strains, changes in epidemiology, virus and vectors impacts arising from climate instability and extreme weather events, and insufficient industry awareness of virus diseases. The pressing need for more resources to focus on addressing these threats is emphasized and recommendations over future research priorities provided.

Global Advances in Tomato Virome Research: Current Status and the Impact of High-Throughput Sequencing

Viruses cause a big fraction of economically important diseases in major crops, including tomato. In the past decade (2011–2020), many emerging or re-emerging tomato-infecting viruses were reported worldwide. In this period, 45 novel viral species were identified in tomato, 14 of which were discovered using high-throughput sequencing (HTS). In this review, we first discuss the role of HTS in these discoveries and its general impact on tomato virome research. We observed that the rate of tomato virus discovery is accelerating in the past few years due to the use of HTS. However, the extent of the post-discovery characterization of viruses is lagging behind and is greater for economically devastating viruses, such as the recently emerged tomato brown rugose fruit virus. Moreover, many known viruses still cause significant economic damages to tomato production. The review of databases and literature revealed at least 312 virus, satellite virus, or viroid species (in 22 families and 39 genera) associated with tomato, which is likely the highest number recorded for any plant. Among those, here, we summarize the current knowledge on the biology, global distribution, and epidemiology of the most important species. Increasing knowledge on tomato virome and employment of HTS to also study viromes of surrounding wild plants and environmental samples are bringing new insights into the understanding of epidemiology and ecology of tomato-infecting viruses and can, in the future, facilitate virus disease forecasting and prevention of virus disease outbreaks in tomato.

Antiviral activity by lecithin-induced fengycin lipopeptides as a potent key substrate against Cucumber mosaic virus

In this study, the effect of different growth substrates on the production of biosurfactants in the PPL strain of Bacillus amyloliquefaciens-a biocontrol agent for diseases affecting pepper and tomato plants-and on the antiviral effect of the PPL strain on Cucumber mosaic virus (CMV)-infected pepper plants was investigated. The multifunctional PPL strain exhibited enhanced growth and increased production of biosurfactants upon lecithin supplementation and consequently exhibited potent anti-CMV activity. The enhanced anti-CMV activity of the lecithin-supplemented PPL culture could be attributed to the antiviral effect as well as to the upregulation of plant defense-related genes. Treatment with pure commercial fengycins elicited a defense response against CMV in pepper plants; this effect was similar to that observed upon treatment with the lecithin-supplemented PPL culture. To the best of our knowledge, this is the first study to report the antiviral activity of lecithin-induced fengycin lipopeptides. These results suggest that the growth substrate affects antimicrobial production by B. amyloliquefaciens PPL, and consequently its antiviral activity.

Metabolic Profile Discriminates and Predicts Arabidopsis Susceptibility to Virus under Field Conditions

As obligatory parasites, plant viruses alter host cellular metabolism. There is a lack of information on the variability of virus-induced metabolic responses among genetically diverse plants in a natural context with daily changing conditions. To decipher the metabolic landscape of plant-virus interactions in a natural setting, twenty-six and ten accessions of Arabidopsis thaliana were inoculated with Turnip mosaic virus (TuMV), in two field experiments over 2 years. The accessions were measured for viral accumulation, above-ground biomass, targeted and untargeted metabolic profiles. The phenotypes of the accessions ranged from susceptibility to resistance. Susceptible and resistant accessions were shown to have different metabolic routes after inoculation. Susceptible genotypes accumulate primary and secondary metabolites upon infection, at the cost of hindered growth. Twenty-one metabolic signatures significantly accumulated in resistant accessions whereas they maintained their growth as mock-inoculated plants without biomass penalty. Metabolic content was demonstrated to discriminate and be highly predictive of the susceptibility of inoculated Arabidopsis. This study is the first to describe the metabolic landscape of plant-virus interactions in a natural setting and its predictive link to susceptibility. It provides new insights on plant-virus interactions. In this undomesticated species and in ecologically realistic conditions, growth and resistance are in a permanent conversation.

A plant reovirus hijacks endoplasmic reticulum-associated degradation machinery to promote efficient viral transmission by its planthopper vector under high temperature conditions

In the field, many insect-borne crop viral diseases are more suitable for maintenance and spread in hot-temperature areas, but the mechanism remains poorly understood. The epidemic of a planthopper (Sogatella furcifera)-transmitted rice reovirus (southern rice black-streaked dwarf virus, SRBSDV) is geographically restricted to southern China and northern Vietnam with year-round hot temperatures. Here, we reported that two factors of endoplasmic reticulum-associated degradation (ERAD) machinery, the heat shock protein DnaJB11 and ER membrane protein BAP31, were activated by viral infection to mediate the adaptation of S. furcifera to high temperatures. Infection and transmission efficiencies of SRBSDV by S. furcifera increased with the elevated temperatures. We observed that high temperature (35°C) was beneficial for the assembly of virus-containing tubular structures formed by nonstructural protein P7-1 of SRBSDV, which facilitates efficient viral transmission by S. furcifera. Both DnaJB11 and BAP31 competed to directly bind to the tubule protein P7-1 of SRBSDV; however, DnaJB11 promoted whereas BAP31 inhibited P7-1 tubule assembly at the ER membrane. Furthermore, the binding affinity of DnaJB11 with P7-1 was stronger than that of BAP31 with P7-1. We also revealed that BAP31 negatively regulated DnaJB11 expression through their direct interaction. High temperatures could significantly upregulate DnaJB11 expression but inhibit BAP31 expression, thereby strongly facilitating the assembly of abundant P7-1 tubules. Taken together, we showed that a new temperature-dependent protein quality control pathway in the ERAD machinery has evolved for strong activation of DnaJB11 for benefiting P7-1 tubules assembly to support efficient transmission of SRBSDV in high temperatures. We thus deduced that ERAD machinery has been hitchhiked by insect-borne crop viruses to enhance their transmission in tropical climates.

Temperature-specific vsiRNA confers RNAi-mediated viral resistance at elevated temperature in Capsicum annuum

Resistance (R) gene-mediated resistance is a robust and efficient antiviral immune system in the plants. Thus, when R-mediated resistance was suppressed at elevated temperatures, resistance towards viruses was expected to be completely collapsed. Nonetheless, the multiplication of Tobacco mosaic virus pathotype P0 (TMV-P0) was inhibited, and TMV-P0 particles were only occasionally present in the systemic leaves of pepper plants (Capsicum annuum). RNAi-mediated RNA silencing is a well-known antiviral immune mechanism. At elevated temperatures, RNAi-mediated antiviral resistance was induced and virus-derived siRNAs (vsiRNAs) were dramatically increased. Through sRNA-sequencing (sRNA-Seq) analysis, we revealed that vsiRNAs derived from TMV-P0 were greatly increased. Intriguingly, virus-infected plants could select the temperature-specific vsiRNAs for antiviral resistance from the amplified vsiRNAs at elevated temperatures. Pre-application of these temperature-specific vsiRNAs endowed antiviral resistance of the plants. Therefore, plants sustain antiviral resistance by activating RNAi-mediated resistance, based on temperature-specific vsiRNAs at elevated temperatures.

Climate change: how it impacts the emergence, transmission, resistance and consequences of viral infections in animals and plants

The ongoing COVID-19 pandemic has made us wonder what led to its occurrence and what can be done to avoid such events in the future. As we document, one changing circumstance that is resulting in the emergence and changing the expression of viral diseases in both plants and animals is climate change. Of note, the rapidly changing environment and weather conditions such as excessive flooding, droughts, and forest fires have raised concerns about the global ecosystem's security, sustainability, and balance. In this review, we discuss the main consequences of climate change and link these to how they impact the appearance of new viral pathogens, how they may facilitate transmission between usual and novel hosts, and how they may also affect the host's ability to manage the infection. We emphasize how changes in temperature and humidity and other events associated with climate change influence the reservoirs of viral infections, their transmission by insects and other intermediates, their survival outside the host as well the success of infection in plants and animals. We conclude that climate change has mainly detrimental consequences for the emergence, transmission, and outcome of viral infections and plead the case for halting and hopefully reversing this dangerous event.

Fine Characterization of a Resistance Phenotype by Analyzing TuYV-Myzus persicae-Rapeseed Interactions

Turnip yellows virus (TuYV), transmitted by Myzus persicae, can be controlled in rapeseed fields by insecticide treatments. However, the recent ban of the neonicotinoids together with the description of pyrethrinoid-resistant aphids has weakened insecticide-based control methods available to farmers. Since the deployment of insecticides in the 1980s, few research efforts were made to breed for rapeseed cultivars resistant to aphid-borne viral diseases. Thus, only few rapeseed cultivars released in Europe were reported to be TuYV-resistant, and the resistance phenotype of these cultivars was poorly characterized. In this study, several epidemiological parameters (infection rate, latency period, etc.) associated to the TuYV-resistance of the cv. Architect were estimated. Results showed a partial resistance phenotype for plants inoculated at the 2-/4-leaves stages and a resistance phenotype for plants inoculated at a more advanced growing stage. Moreover, analysis of infected plants highlighted (i) a poor quality of infected cv. Architect as a source of virus for transmission and (ii) an extended latency period for infected plants. Thus, dynamics of virus spread in the field should to be slower for Architect compared to susceptible rapeseed cultivars, which should lead to the maintenance of a higher proportion of healthy plants in the field.

Global Plant Virus Disease Pandemics and Epidemics

The world's staple food crops, and other food crops that optimize human nutrition, suffer from global virus disease pandemics and epidemics that greatly diminish their yields and/or produce quality. This situation is becoming increasingly serious because of the human population's growing food requirements and increasing difficulties in managing virus diseases effectively arising from global warming. This review provides historical and recent information about virus disease pandemics and major epidemics that originated within different world regions, spread to other continents, and now have very wide distributions. Because they threaten food security, all are cause for considerable concern for humanity. The pandemic disease examples described are six (maize lethal necrosis, rice tungro, sweet potato virus, banana bunchy top, citrus tristeza, plum pox). The major epidemic disease examples described are seven (wheat yellow dwarf, wheat streak mosaic, potato tuber necrotic ringspot, faba bean necrotic yellows, pepino mosaic, tomato brown rugose fruit, and cucumber green mottle mosaic). Most examples involve long-distance virus dispersal, albeit inadvertent, by international trade in seed or planting material. With every example, the factors responsible for its development, geographical distribution and global importance are explained. Finally, an overall explanation is given of how to manage global virus disease pandemics and epidemics effectively.

Disease Pandemics and Major Epidemics Arising from New Encounters between Indigenous Viruses and Introduced Crops

Virus disease pandemics and epidemics that occur in the world’s staple food crops pose a major threat to global food security, especially in developing countries with tropical or subtropical climates. Moreover, this threat is escalating rapidly due to increasing difficulties in controlling virus diseases as climate change accelerates and the need to feed the burgeoning global population escalates. One of the main causes of these pandemics and epidemics is the introduction to a new continent of food crops domesticated elsewhere, and their subsequent invasion by damaging virus diseases they never encountered before. This review focusses on providing historical and up-to-date information about pandemics and major epidemics initiated by spillover of indigenous viruses from infected alternative hosts into introduced crops. This spillover requires new encounters at the managed and natural vegetation interface. The principal virus disease pandemic examples described are two (cassava mosaic, cassava brown streak) that threaten food security in sub-Saharan Africa (SSA), and one (tomato yellow leaf curl) doing so globally. A further example describes a virus disease pandemic threatening a major plantation crop producing a vital food export for West Africa (cacao swollen shoot). Also described are two examples of major virus disease epidemics that threaten SSA’s food security (rice yellow mottle, groundnut rosette). In addition, brief accounts are provided of two major maize virus disease epidemics (maize streak in SSA, maize rough dwarf in Mediterranean and Middle Eastern regions), a major rice disease epidemic (rice hoja blanca in the Americas), and damaging tomato tospovirus and begomovirus disease epidemics of tomato that impair food security in different world regions. For each pandemic or major epidemic, the factors involved in driving its initial emergence, and its subsequent increase in importance and geographical distribution, are explained. Finally, clarification is provided over what needs to be done globally to achieve effective management of severe virus disease pandemics and epidemics initiated by spillover events.

Potato virus Y and Potato leafroll virus management under climate change in sub-Saharan Africa

Potato has increased in importance as a staple food in sub-Saharan Africa, where its production is faced with a multitude of challenges, including plant disease development and spread under changing climatic conditions. The economically most important plant viruses affecting potatoes globally are Potato virus Y (PVY) and Potato leafroll virus (PLRV). Disease management relies mostly on the use of insecticides, cultural control and seed certification schemes. A major obstacle in many sub-Saharan Africa countries is the availability of disease-free quality seed potatoes. Establishment and implementation of quality control through specialised seed production systems and certification schemes is critical to improve seed potato quality and reduce PVY and PLRV sources. Seed could be further improved by breeding virus-resistant varieties adapted to different environmental conditions combined with management measures tailored for smallholder or commercial farmers to specific agricultural requirements. Innovative technologies – including more sensitive testing, remote sensing, machine learning and predictive models – provide new tools for the management of PVY and PLRV, but require support for adoption and implementation in sub-Saharan Africa.

Emergence and Full Genome Analysis of Tomato Torrado Virus in South Africa

Emerging pests and diseases are a major threat to food production worldwide. In a recent survey, Tomato torrado virus (ToTV) was identified on tomato crops in the Limpopo province of South Africa and a first report of the disease was published. In this follow-up study, the full genome sequence of a tomato-infecting isolate of ToTV from South Africa was elucidated. High-throughput sequencing was used to generate the full genome of ToTV infecting tomato crops in South Africa. The longest contig obtained for the RNA-1 and RNA-2 genome of ToTV was comprised of 7420 and 5381 nucleotides (nt), respectively. Blast analysis of the RNA-1 sequence of ToTV from South Africa (ToT-186) matched 99% to a Spanish and Polish isolate; the RNA-2 segment of ToTV from South Africa (ToT-186) matched 99% to ToTV isolates from Italy and Poland, respectively. The information presented in this study will go a long way towards better understanding the emergence and spread of ToTV and devising sustainable management of ToTV diseases.

The effects of regional climatic condition on the spread of COVID-19 at global scale

The pandemic outbreak of the novel coronavirus epidemic disease (COVID-19) is spreading like a diffusion-reaction in the world and almost 208 countries and territories are being affected around the globe. It became a sever health and socio-economic problem, while the world has no vaccine to combat this virus. This research aims to analyze the connection between the fast spread of COVID-19 and regional climate parameters over a global scale. In this research, we collected the data of COVID-19 cases from the time of 1st reported case to the 5th June 2020 in different affected countries and regional climatic parameters data from January 2020 to 5th June 2020. It was found that most of the countries located in the relatively lower temperature region show a rapid increase in the COVID-19 cases than the countries locating in the warmer climatic regions despite their better socio-economic conditions. A correlation between metrological parameters and COVID-19 cases was observed. Average daylight hours are correlated to total the COVID-19 cases with a coefficient of determination of 0.42, while average high-temperature shows a correlation of 0.59 and 0.42 with total COVID-19 cases and death cases respectively. The finding of the study will help international health organizations and local administrations to combat and well manage the spread of COVID-19.

Comparative study on three viral enrichment approaches based on RNA extraction for plant virus/viroid detection using high-throughput sequencing

High-throughput sequencing (HTS) has become increasingly popular as virus diagnostic tool. It has been used to detect and identify plant viruses and viroids in different types of matrices and tissues. A viral sequence enrichment method prior to HTS is required to increase the viral reads in the generated data to ease the bioinformatic analysis of generated sequences. In this study, we compared the sensitivity of three viral enrichment approaches, i.e. double stranded RNA (dsRNA), ribosomal RNA depleted total RNA (ribo-depleted totRNA) and small RNA (sRNA) for plant virus/viroid detection, followed by sequencing on MiSeq and NextSeq Illumina platforms. The three viral enrichment approaches used here enabled the detection of all viruses/viroid used in this study. When the data was normalised, the recovered viral/viroid nucleotides and depths were depending on the viral genome and the enrichment method used. Both dsRNA and ribo-depleted totRNA approaches detected a divergent strain of Wuhan aphid virus 2 that was not expected in this sample. Additionally, Vicia cryptic virus was detected in the data of dsRNA and sRNA approaches only. The results suggest that dsRNA enrichment has the highest potential to detect and identify plant viruses and viroids. The dsRNA approach used here detected all viruses/viroid, consumed less time, was lower in cost, and required less starting material. Therefore, this approach appears to be suitable for diagnostics laboratories.

Modulation of disease severity by plant positive-strand RNA viruses: The complex interplay of multifunctional viral proteins, subviral RNAs and virus-associated RNAs with plant signaling pathways and defense responses

Plant viruses induce a range of symptoms of varying intensity, ranging from severe systemic necrosis to mild or asymptomatic infection. Several evolutionary constraints drive virus virulence, including the dependence of viruses on host factors to complete their infection cycle, the requirement to counteract or evade plant antiviral defense responses and the mode of virus transmission. Viruses have developed an array of strategies to modulate disease severity. Accumulating evidence has highlighted not only the multifunctional role that viral proteins play in disrupting or highjacking plant factors, hormone signaling pathways and intracellular organelles, but also the interaction networks between viral proteins, subviral RNAs and/or other viral-associated RNAs that regulate disease severity. This review focusses on positive-strand RNA viruses, which constitute the majority of characterized plant viruses. Using well-characterized viruses with different genome types as examples, recent advances are discussed as well as knowledge gaps and opportunities for further research.

Management of yellow dwarf disease in Europe in a post-neonicotinoid agriculture

Barley/cereal yellow dwarf viruses (YDVs) cause yellow dwarf disease (YDD), which is a continuous risk to cereals production worldwide. These viruses cause leaf yellowing and stunting, resulting in yield reductions of up to 80%. YDVs have been a consistent but low-level problem in European cereal cultivation for the last three decades, mostly due to the availability of several effective insecticides (largely pyrethroids and more recently neonicotinoids) against aphid vectors. However, this has changed recently, with many insecticides being lost, culminating in a recent European Union (EU) regulation prohibiting outdoor use of the neonicotinoid-insecticide compounds. This change is coupled with the growing challenge of insecticide-resistant aphids, the lack of genetic resources against YDVs, and a knowledge deficit around the parameters responsible for the emergence and spread of YDD. This means that economic sustainability of cereal cultivation in several European countries including France and United Kingdom is now again threatened by this aphid-vectored viral disease. In this review, we summarize the current knowledge on the YDV pathosystem, describe management options against YDD, analyse the impacts of the neonicotinoid ban in Europe, and consider future strategies to control YDV. © 2020 Society of Chemical Industry.

High-Throughput Sequencing Facilitates Discovery of New Plant Viruses in Poland

Viruses cause epidemics on all major crops of agronomic importance, and a timely and accurate identification is essential for control. High throughput sequencing (HTS) is a technology that allows the identification of all viruses without prior knowledge on the targeted pathogens. In this paper, we used HTS technique for the detection and identification of different viral species occurring in single and mixed infections in plants in Poland. We analysed various host plants representing different families. Within the 20 tested samples, we identified a total of 13 different virus species, including those whose presence has not been reported in Poland before: clover yellow mosaic virus (ClYMV) and melandrium yellow fleck virus (MYFV). Due to this new finding, the obtained sequences were compared with others retrieved from GenBank. In addition, cucurbit aphid-borne yellows virus (CABYV) was also detected, and due to the recent occurrence of this virus in Poland, a phylogenetic analysis of these new isolates was performed. The analysis revealed that CABYV population is highly diverse and the Polish isolates of CABYV belong to two different phylogenetic groups. Our results showed that HTS-based technology is a valuable diagnostic tool for the identification of different virus species originating from variable hosts, and can provide rapid information about the spectrum of plant viruses previously not detected in a region.

Effects of a changing environment on the defenses of plants to viruses

Since their appearance, plants have lived and evolved within changing environments that were determined by a host of abiotic and biotic factors. It is in this evolutionary context that both, the mechanisms of defense by plants against viruses and the viral reprogramming of plant routes were established, which combined define the outcomes of compatible infections. Current alterations in the chemistry of the atmosphere are causing changes in the global context in which plants and viruses interact that are unprecedented not in their nature but in their pace. We discuss here the potential reach of environment changes taking place now, and how the main abiotic parameters that are driving them can affect defense responses of plants to viruses in compatible infections.

Plant Viruses Infecting Solanaceae Family Members in the Cultivated and Wild Environments: A Review

Plant viruses infecting crop species are causing long-lasting economic losses and are endangering food security worldwide. Ongoing events, such as climate change, changes in agricultural practices, globalization of markets or changes in plant virus vector populations, are affecting plant virus life cycles. Because farmer’s fields are part of the larger environment, the role of wild plant species in plant virus life cycles can provide information about underlying processes during virus transmission and spread. This review focuses on the Solanaceae family, which contains thousands of species growing all around the world, including crop species, wild flora and model plants for genetic research. In a first part, we analyze various viruses infecting Solanaceae plants across the agro-ecological interface, emphasizing the important role of virus interactions between the cultivated and wild zones as global changes affect these environments on both local and global scales. To cope with these changes, it is necessary to adjust prophylactic protection measures and diagnostic methods. As illustrated in the second part, a complex virus research at the landscape level is necessary to obtain relevant data, which could be overwhelming. Based on evidence from previous studies we conclude that Solanaceae plant communities can be targeted to address complete life cycles of viruses with different life strategies within the agro-ecological interface. Data obtained from such research could then be used to improve plant protection methods by taking into consideration environmental factors that are impacting the life cycles of plant viruses.

From foes to friends: Viral infections expand the limits of host phenotypic plasticity

Phenotypic plasticity enables organisms to survive in the face of unpredictable environmental stress. Intimately related to the notion of phenotypic plasticity is the concept of the reaction norm that places phenotypic plasticity in the context of a genotype-specific response to environmental gradients. Whether reaction norms themselves evolve and which factors might affect their shape has been the object of intense debates among evolutionary biologists along the years. Since their discovery, viruses have been considered as pathogens. However, new viromic techniques and a shift in conceptual paradigms are showing that viruses are mostly non-pathogenic ubiquitous entities. Recent studies have shown how viral infections can even be beneficial for their hosts. This may happen especially in the context of stressed hosts, where the virus infection can induce beneficial changes in the host's physiological homeostasis, hence changing the shape of the reaction norm. Despite the fact that underlying physiological mechanisms and evolutionary dynamics are still not well understood, such beneficial interactions are being discovered in a growing number of plant-virus systems. Here, we aim to review these disperse studies and place them into the context of phenotypic plasticity and the evolution of reaction norms. This is an emerging field that is posing many questions that still need to be properly answered. The answers would clearly interest virologists, plant pathologists and evolutionary biologists and likely they will suggest possible future biotechnological applications, including the development of crops with higher survival rates and yield under adverse environmental situations.

Light Intensity Modulates the Efficiency of Virus Seed Transmission through Modifications of Plant Tolerance

Increased light intensity has been predicted as a major consequence of climate change. Light intensity is a critical resource involved in many plant processes, including the interaction with viruses. A central question to plant-virus interactions is understanding the determinants of virus dispersal among plants. However, very little is known on the effect of environmental factors on virus transmission, particularly through seeds. The fitness of seed-transmitted viruses is highly dependent on host reproductive potential, and requires higher virus multiplication in reproductive organs. Thus, environmental conditions that favor reduced virus virulence without controlling its level of within-plant multiplication (i.e., tolerance) may enhance seed transmission. We tested the hypothesis that light intensity conditions that enhance plant tolerance promote virus seed transmission. To do so, we challenged 18 Arabidopsis thaliana accessions with Turnip mosaic virus (TuMV) and Cucumber mosaic virus (CMV) under high and low light intensity. Results indicated that higher light intensity increased TuMV multiplication and/or plant tolerance, which was associated with more efficient seed transmission. Conversely, higher light intensity reduced plant tolerance and CMV multiplication, and had no effect on seed transmission. This work provides novel insights on how environmental factors modulate plant virus transmission and contributes to understand the underlying processes.

Global Dimensions of Plant Virus Diseases: Current Status and Future Perspectives

Viral diseases provide a major challenge to twenty-first century agriculture worldwide. Climate change and human population pressures are driving rapid alterations in agricultural practices and cropping systems that favor destructive viral disease outbreaks. Such outbreaks are strikingly apparent in subsistence agriculture in food-insecure regions. Agricultural globalization and international trade are spreading viruses and their vectors to new geographical regions with unexpected consequences for food production and natural ecosystems. Due to the varying epidemiological characteristics of diverent viral pathosystems, there is no one-size-fits-all approach toward mitigating negative viral disease impacts on diverse agroecological production systems. Advances in scientific understanding of virus pathosystems, rapid technological innovation, innovative communication strategies, and global scientific networks provide opportunities to build epidemiologic intelligence of virus threats to crop production and global food security. A paradigm shift toward deploying integrated, smart, and eco-friendly strategies is required to advance virus disease management in diverse agricultural cropping systems.

Zucchini yellow mosaic virus Genomic Sequences from Papua New Guinea: Lack of Genetic Connectivity with Northern Australian or East Timorese Genomes, and New Recombination Findings

Zucchini yellow mosaic virus (ZYMV) isolates were obtained in Papua New Guinea (PNG) from cucumber (Cucumis sativus) or pumpkin (Cucurbita spp.) plants showing mosaic symptoms growing at Kongop in the Mount Hagen District, Western Highlands Province, or Zage in the Goroka District, Eastern Highlands Province. The samples were blotted onto FTA cards, which were sent to Australia, where they were subjected to high-throughput sequencing. When the coding regions of the nine new ZYMV genomic sequences found were compared with those of 64 other ZYMV sequences from elsewhere, they grouped together, forming new minor phylogroup VII within ZYMV's major phylogroup A. Genetic connectivity was lacking between ZYMV genomic sequences from PNG and its neighboring countries, Australia and East Timor; the closest match between a PNG and any other genomic sequence was a 92.8% nucleotide identity with a sequence in major phylogroup A's minor phylogroup VI from Japan. When the RDP5.2 recombination analysis program was used to compare 66 ZYMV sequences, evidence was obtained of 30 firm recombination events involving 41 sequences, and all isolates from PNG were recombinants. There were 21 sequences without recombination events in major phylogroup A, whereas there were only 4 such sequences within major phylogroup B. ZYMV's P1, Cl, N1a-Pro, P3, CP, and NIb regions contained the highest evidence of recombination breakpoints. Following removal of recombinant sequences, seven minor phylogroups were absent (I, III, IV, V, VI, VII, and VIII), leaving only minor phylogroups II and IX. By contrast, when a phylogenetic tree was constructed using recombinant sequences with their recombinationally derived tracts removed before analysis, five previous minor phylogroups remained unchanged within major phylogroup A (II, III, IV, V, and VII) while four formed two new merged phylogroups (I/VI and VIII/IX). Absence of genetic connectivity between PNG, Australian, and East Timorese ZYMV sequences, and the 92.8% nucleotide identity between a PNG sequence and the closest sequence from elsewhere, suggest that a single introduction may have occurred followed by subsequent evolution to adapt to the PNG environment. The need for enhanced biosecurity measures to protect against potentially damaging virus movements crossing the seas separating neighboring countries in this region of the world is discussed.

Genetic Connectivity Between Papaya Ringspot Virus Genomes from Papua New Guinea and Northern Australia, and New Recombination Insights

Isolates of papaya ringspot virus (PRSV) were obtained from plants of pumpkin (Cucurbita spp.) or cucumber (Cucumis sativus) showing mosaic symptoms growing at Zage in Goroka District in the Eastern Highland Province of Papua New Guinea (PNG) or Bagl in the Mount Hagen District, Western Highlands Province. The samples were sent to Australia on FTA cards where they were subjected to High Throughput Sequencing (HTS). When the coding regions of the six new PRSV genomic sequences obtained via HTS were compared with those of 54 other complete PRSV sequences from other parts of the world, all six grouped together with the 12 northern Australian sequences within major phylogroup B minor phylogroup I, the Australian sequences coming from three widely dispersed locations spanning the north of the continent. Notably, none of the PNG isolates grouped with genomic sequences from the nearby country of East Timor in phylogroup A. The closest genetic match between Australian and PNG sequences was a nucleotide (nt) sequence identity of 96.9%, whereas between PNG and East Timorese isolates it was only 83.1%. These phylogenetic and nt identity findings demonstrate genetic connectivity between PRSV populations from PNG and Australia. Recombination analysis of the 60 PRSV sequences available revealed evidence of 26 recombination events within 18 isolates, only four of which were within major phylogroup B and none of which were from PNG or Australia. Within the recombinant genomes, the P1, Cl, NIa-Pro, NIb, 6K2, and 5'UTR regions contained the highest numbers of recombination breakpoints. After removal of nonrecombinant sequences, four minor phylogroups were lost (IV, VII, VIII, XV), only one of which was in phylogroup B. When genome regions from which recombinationally derived tracts of sequence were removed from recombinants prior to alignment with nonrecombinant genomes, seven previous minor phylogroups within major phylogroup A, and two within major phylogroup B, merged either partially or entirely forming four merged minor phylogroups. The genetic connectivity between PNG and northern Australian isolates and absence of detectable recombination within either group suggests that PRSV isolates from East Timor, rather than PNG, might pose a biosecurity threat to northern Australian agriculture should they prove more virulent than those already present.

Prevalence and Incidence of Yellow Dwarf Viruses Across a Climatic Gradient: A Four-Year Field Study in Southeastern Australia

Yellow dwarf viruses (YDVs) form a complex of economically important pathogens that affect cereal production worldwide, reducing yield and quality. The prevalence and incidence of YDVs including barley yellow dwarf viruses (BYDV-PAV and BYDV-MAV) and cereal yellow dwarf virus (CYDV-RPV) in cereal fields in Victoria, Australia were measured. As temperature decreases and rainfall increases from north to south in Victoria, fields in three geographical regions were evaluated to determine potential differences in virus prevalence and incidence across the weather gradient. Cereal samples randomly collected from each field during spring for four consecutive years (2014-2017) were tested for BYDV-PAV, BYDV-MAV, and CYDV-RPV using tissue blot immunoassay. BYDV-PAV was the most prevalent YDV species overall and had the highest overall mean incidence. Higher temperature and lower rainfall were associated with reduced prevalence and incidence of YDVs as the northern region, which is hotter and drier, had a 17-fold decrease in virus incidence compared with the cooler and wetter regions. Considerable year-to-year variation in virus prevalence and incidence was observed. This study improves our understanding of virus epidemiology, which will aid the development of more targeted control measures and predictive models. It also highlights the need to monitor for YDVs and their vectors over multiple years to assess the level of risk and to make more informed and appropriate disease management decisions.

Anthropogenic Impacts on Meiosis in Plants

As the human population grows and continues to encroach on the natural environment, organisms that form part of such ecosystems are becoming increasingly exposed to exogenous anthropogenic factors capable of changing their meiotic landscape. Meiotic recombination generates much of the genetic variation in sexually reproducing species and is known to be a highly conserved pathway. Environmental stresses, such as variations in temperature, have long been known to change the pattern of recombination in both model and crop plants, but there are other factors capable of causing genome damage, infertility and meiotic abnormalities. Our agrarian expansion and our increasing usage of agrochemicals unintentionally affect plants via groundwater contamination or spray drift; our industrial developments release heavy metals into the environment; pathogens are spread by climate change and a globally mobile population; imperfect waste treatment plants are unable to remove chemical and pharmaceutical residues from sewage leading to the release of xenobiotics, all with potentially deleterious meiotic effects. In this review, we discuss the major classes of exogenous anthropogenic factors known to affect meiosis in plants, namely environmental stresses, agricultural inputs, heavy metals, pharmaceuticals and pathogens. The possible evolutionary fate of plants thrust into their new anthropogenically imposed environments are also considered.