Geminivirus mixed infection on pepper plants: synergistic interaction between PHYVV and PepGMV

N Protein of Tomato Spotted Wilt Virus Proven to Be Antagonistic Against Tomato Yellow Leaf Curl Virus in Nicotiana benthamiana

Two phylogenetically unrelated viruses transmitted by different insect vectors, tomato spotted wilt virus (TSWV) and tomato yellow leaf curl virus (TYLCV), are major threats to tomato and other vegetable production. Although co-infections of TSWV and TYLCV on the same host plant have been reported on numerous occasions, there is still lack of research attempting to elucidate the mechanisms underlying the relationship between two viruses when they coexist in the same tomato or other plants. After assessing the effect of four TSWV-coded proteins on suppressing TYLCV in TSWV N transgenic Nicotiana benthamiana seedlings, the TSWV N protein proved to be effective in reducing TYLCV quantity and viral symptoms. Western blot analysis indicated that TSWV N was involved in down-regulating the expression level of the V1, C3, and C4 proteins of TYLCV, among which V1 was the most significantly suppressed one. Moreover, TSWV N was confirmed to reduce TYLCV V1 within both nucleus and cytoplasm, but a greater suppression was observed in cytoplasm. The co-immunoprecipitation and mass spectrometry identified 244 differential proteins from the TYLCV-infected TSWV N transgenic N. benthamiana seedling. These proteins pertaining to energy metabolism pathways were enriched, suggesting that TSWV N could inhibit TYLCV through competing for energy or regulating energy-related metabolism. The evidence presented here offers a novel perspective that will facilitate a comprehensive understanding of virus-virus and virus-host interactions, as well as a potential strategy for plant virus control through using TSWV N in the near future.

Exploring the Global Trends of Bacillus, Trichoderma and Entomopathogenic Fungi for Pathogen and Pest Control in Chili Cultivation

Chili, renowned globally and deeply ingrained in various cultures. Regrettably, the onset of diseases instigated by pests and pathogens has inflicted substantial losses on chili crops, with some farms experiencing complete production decimation. Challenges confronting chili cultivation include threats from pathogenic microbes like Xanthomonas, Fusarium, Phytophthora, Verticillium, Rhizoctonia, Colletotrichium and Viruses, alongside pests such as whiteflies, mites, thrips, aphids, and fruit flies. While conventional farming practices often resort to chemical pesticides to combat these challenges, their utilization poses substantial risks to both human health and the environment. In response to this pressing issue, this review aims to evaluate the potential of microbe-based biological control as eco-friendly alternatives to chemical pesticides for chili cultivation. Biocontrol agents such as Bacillus spp., Trichoderma spp., and entomopathogenic fungi present safer and more environmentally sustainable alternatives to chemical pesticides. However, despite the recognised potential of biocontrol agents, research on their efficacy in controlling the array of pests and pathogens affecting chili farming remains limited. This review addresses this gap by evaluating the efficiency of biocontrol agents, drawing insights from existing studies conducted in other crop systems, regarding pest and pathogen management. Notably, an analysis of Scopus publications revealed fewer than 30 publications in 2023 focused on these three microbial agents. Intriguingly, India, as the world's largest chili producer, leads in the number of publications concerning Bacillus spp., Trichoderma spp., and entomopathogenic fungi in chili cultivation. Further research on microbial agents is imperative to mitigate infections and reduce reliance on chemical pesticides for sustainable chili production.

Genomic Characterization and Molecular Detection of Rehmannia Allexivirus Virus, a Novel Allexivirus Infecting Rehmannia glutinosa

Rehmannia glutinosa is one of the most important medicinal plants in China and is affected by viral diseases. In this study, a new virus tentatively named Rehmannia Allexivirus virus (ReAV) was identified through high-throughput sequencing, reverse-transcription polymerase chain reaction (RT-PCR), and Sanger sequencing. The complete genome length was 7297 nt and it contained five open reading frames (ORFs) encoding replicase, triple gene block 1(TGB1), TGB2, TGB3, and coat protein (CP). The replicase and CP presented nucleotide homology ranges of 59.9-65.2% and 47.5-55.5% between the nine ReAV isolates and the other 12 species of the genus Allexivirus. In the nine isolates, ReAV-20 and ReAV-31 isolates showed breakpoints in the replicase and CP regions, respectively. The other isolates shared 87.2-96.5% nt with the whole genome nucleotide identity. The phylogenetic tree showed that seven ReAV isolates based on replicase, CP, and whole genome sequences were clustered in the same branch and were related to the genus Allexivirus. The ReAV detection rates for 60 R. glutinosa samples were 73.3-81.7% through RT-PCR using primers targeting the replicase or CP genes. These results demonstrate that ReAV is the dominant virus in R. glutinosa. This study provides important evidence for understanding viruses infecting R. glutinosa and for establishing efficient strategies to prevent viral spread.

Begomovirus Inoculation in Arabidopsis and Cassava

The use of infectious clones to inoculate plant viruses allows for controlled studies that lead to a better understanding of plant-virus interactions. The main methods used for laboratory inoculation of geminiviruses are agroinoculation and biolistics. We describe how to successfully inoculate geminiviruses, focusing on Arabidopsis as a model plant and cassava as a crop.

Current status, breeding strategies and future prospects for managing chilli leaf curl virus disease and associated begomoviruses in Chilli (Capsicum spp.)

Chilli leaf curl virus disease caused by begomoviruses, has emerged as a major threat to global chilli production, causing severe yield losses and economic harm. Begomoviruses are a highly successful and emerging group of plant viruses that are primarily transmitted by whiteflies belonging to the Bemisia tabaci complex. The most effective method for mitigating chilli leaf curl virus disease losses is breeding for host resistance to Begomovirus. This review highlights the current situation of chilli leaf curl virus disease and associated begomoviruses in chilli production, stressing the significant issues that breeders and growers confront. In addition, the various breeding methods used to generate begomovirus resistant chilli cultivars, and also the complicated connections between the host plant, vector and the virus are discussed. This review highlights the importance of resistance breeding, emphasising the importance of multidisciplinary approaches that combine the best of traditional breeding with cutting-edge genomic technologies. subsequently, the article highlights the challenges that must be overcome in order to effectively deploy begomovirus resistant chilli varieties across diverse agroecological zones and farming systems, as well as understanding the pathogen thus providing the opportunities for improving the sustainability and profitability of chilli production.

Specific Nucleotides in the Common Region of the Begomovirus Tomato Rugose Mosaic Virus (ToRMV) Are Responsible for the Negative Interference over Tomato Severe Rugose Virus (ToSRV) in Mixed Infection

Mixed infection between two or more begomoviruses is commonly found in tomato fields and can affect disease outcomes by increasing symptom severity and viral accumulation compared with single infection. Viruses that affect tomato include tomato severe rugose virus (ToSRV) and tomato rugose mosaic virus (ToRMV). Previous work showed that in mixed infection, ToRMV negatively affects the infectivity and accumulation of ToSRV. ToSRV and ToRMV share a high degree of sequence identity, including cis-elements in the common region (CR) and their specific recognition sites (iteron-related domain, IRD) within the Rep gene. Here, we investigated if divergent sites in the CR and IRD are involved in the interaction between these two begomoviruses. ToSRV clones were constructed containing the same nucleotides as ToRMV in the CR (ToSRV-A(ToR:CR)), IRD (ToSRV-A(ToR:IRD)) and in both regions (ToSRV-A(ToR:CR+IRD)). When plants were co-inoculated with ToRMV and ToSRV-A(ToR:IRD), the infectivity and accumulation of ToSRV were negatively affected. In mixed inoculation of ToRMV with ToSRV-A(ToR:CR), high infectivity of both viruses and high DNA accumulation of ToSRV-A(ToR:CR) were observed. A decrease in viral accumulation was observed in plants inoculated with ToSRV-A(ToR:CR+IRD). These results indicate that differences in the CR, but not the IRD, are responsible for the negative interference of ToRMV on ToSRV.

Fast and High-Efficiency Synthesis of Capsanthin in Pepper by Transient Expression of Geminivirus

The color of the chili fruit is an important factor that determines the quality of the chili, as red chilies are more popular among consumers. The accumulation of capsanthin is the main cause of reddening of the chili fruit. Capsanthin is an important metabolite in carotenoid metabolism, and its production level is closely linked to the expression of the genes for capsanthin/capsorubin synthase (CCS) and carotenoid hydroxylase (CrtZ). We reported for the first time that the synthesis of capsanthin in chili was enhanced by using a geminivirus (Bean Yellow Dwarf Virus). By expressing heterologous β-carotenoid hydroxylase (CrtZ) and β-carotenoid ketolase (CrtW) using codon optimization, the transcription level of the CCS gene and endogenous CrtZ was directly increased. This leads to the accumulation of a huge amount of capsanthin in a very short period of time. Our results provide a platform for the rapid enhancement of endogenous CCS activity and capsanthin production using geminivirus in plants.

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.

Effects of Host Plants and Their Infection Status on Acquisition and Inoculation of A Plant Virus by Its Hemipteran Vector

Whitefly, Bemisia tabaci Gennadius (B cryptic species), transmits cucurbit leaf crumple virus (CuLCrV) in a persistent fashion. CuLCrV affects several crops such as squash and snap bean in the southeastern United States. CuLCrV is often found as a mixed infection with whitefly transmitted criniviruses, such as cucurbit yellow stunting disorder virus (CYSDV) in hosts such as squash, or as a single infection in hosts such as snap bean. The implications of different host plants (inoculum sources) with varying infection status on CuLCrV transmission/epidemics is not clear. This study conducted a series of whitefly mediated CuLCrV transmission experiments. In the first experiment, three plants species: squash, snap bean, and tobacco were inoculated by whiteflies feeding on field-collected mixed-infected squash plants. In the second experiment, three plant species, namely squash, snap bean, and tobacco with varying infection status (squash infected with CuLCrV and CYSDV and snap bean and tobacco infected with CuLCrV), were used as inoculum sources. In the third experiment, squash plants with differential CuLCrV accumulation levels and infection status (either singly infected with CuLCrV or mixed infected with CuLCrV and CYSDV) were used as inoculum sources. Irrespective of plant species and its infection status, CuLCrV accumulation in whiteflies was dependent upon the CuLCrV accumulation in the inoculum source plants. Furthermore, differential CuLCrV accumulation in whiteflies resulted in differential transmission, CuLCrV accumulation, and disease phenotype in the recipient squash plants. Overall, results demonstrate that whitefly mediated CuLCrV transmission between host plants follows a virus density dependent phenomenon with implications for epidemics.

Virus-virus interactions alter the mechanical transmissibility and host range of begomoviruses

Introduction

Begomoviruses are mainly transmitted by whiteflies. However, a few begomoviruses can be transmitted mechanically. Mechanical transmissibility affects begomoviral distribution in the field.

Materials and methods

In this study, two mechanically transmissible begomoviruses, tomato leaf curl New Delhi virus-oriental melon isolate (ToLCNDV-OM) and tomato yellow leaf curl Thailand virus (TYLCTHV), and two nonmechanically transmissible begomoviruses, ToLCNDV-cucumber isolate (ToLCNDV-CB) and tomato leaf curl Taiwan virus (ToLCTV), were used to study the effects of virus-virus interactions on mechanical transmissibility.

Results

Nicotiana benthamiana and host plants were coinoculated through mechanical transmission with inoculants derived from plants that were mix-infected or inoculants derived from individually infected plants, and the inoculants were mixed immediately before inoculation. Our results showed that ToLCNDV-CB was mechanically transmitted with ToLCNDV-OM to N. benthamiana, cucumber, and oriental melon, whereas ToLCTV was mechanically transmitted with TYLCTHV to N. benthamiana and tomato. For crossing host range inoculation, ToLCNDV-CB was mechanically transmitted with TYLCTHV to N. benthamiana and its nonhost tomato, while ToLCTV with ToLCNDV-OM was transmitted to N. benthamiana and its nonhost oriental melon. For sequential inoculation, ToLCNDV-CB and ToLCTV were mechanically transmitted to N. benthamiana plants that were either preinfected with ToLCNDV-OM or TYLCTHV. The results of fluorescence resonance energy transfer analyses showed that the nuclear shuttle protein of ToLCNDV-CB (CBNSP) and the coat protein of ToLCTV (TWCP) localized alone to the nucleus. When coexpressed with movement proteins of ToLCNDV-OM or TYLCTHV, CBNSP and TWCP relocalized to both the nucleus and the cellular periphery and interacted with movement proteins.

Discussion

Our findings indicated that virus-virus interactions in mixed infection circumstances could complement the mechanical transmissibility of nonmechanically transmissible begomoviruses and alter their host range. These findings provide new insight into complex virus-virus interactions and will help us to understand the begomoviral distribution and to reevaluate disease management strategies in the field.

Comparative Genome Analysis of Old World and New World TYLCV Reveals a Biasness toward Highly Variable Amino Acids in Coat Protein

Begomoviruses, belonging to the family Geminiviridae and the genus Begomovirus, are DNA viruses that are transmitted by whitefly Bemisia tabaci (Gennadius) in a circulative persistent manner. They can easily adapt to new hosts and environments due to their wide host range and global distribution. However, the factors responsible for their adaptability and coevolutionary forces are yet to be explored. Among BGVs, TYLCV exhibits the broadest range of hosts. In this study, we have identified variable and coevolving amino acid sites in the proteins of Tomato yellow leaf curl virus (TYLCV) isolates from Old World (African, Indian, Japanese, and Oceania) and New World (Central and Southern America). We focused on mutations in the coat protein (CP), as it is highly variable and interacts with both vectors and host plants. Our observations indicate that some mutations were accumulating in Old World TYLCV isolates due to positive selection, with the S149N mutation being of particular interest. This mutation is associated with TYLCV isolates that have spread in Europe and Asia and is dominant in 78% of TYLCV isolates. On the other hand, the S149T mutation is restricted to isolates from Saudi Arabia. We further explored the implications of these amino acid changes through structural modeling. The results presented in this study suggest that certain hypervariable regions in the genome of TYLCV are conserved and may be important for adapting to different host environments. These regions could contribute to the mutational robustness of the virus, allowing it to persist in different host populations.

Visual tracking of viral infection dynamics reveals the synergistic interactions between cucumber mosaic virus and broad bean wilt virus 2

Cucumber mosaic virus (CMV) is one of the most prevalent plant viruses in the world, and causes severe damage to various crops. CMV has been studied as a model RNA virus to better understand viral replication, gene functions, evolution, virion structure, and pathogenicity. However, CMV infection and movement dynamics remain unexplored due to the lack of a stable recombinant virus tagged with a reporter gene. In this study, we generated a CMV infectious cDNA construct tagged with a variant of the flavin-binding LOV photoreceptor (iLOV). The iLOV gene was stably maintained in the CMV genome after more than four weeks of three serial passages between plants. Using the iLOV-tagged recombinant CMV, we visualized CMV infection and movement dynamics in living plants in a time course manner. We also examined whether CMV infection dynamics is influenced by co-infection with broad bean wilt virus 2 (BBWV2). Our results revealed that no spatial interference occurred between CMV and BBWV2. Specifically, BBWV2 facilitated the cell-to-cell movement of CMV in the upper young leaves. In addition, the BBWV2 accumulation level increased after co-infection with CMV.

Identification of begomoviruses associated with the insect vector Bemisia tabaci and various host plants on Java Island, Indonesia

Begomoviruses are economically important plant viruses and are transmitted by Bemisia tabaci which is a complex of various cryptic species. However, it is uncertain whether most begomoviruses that infect host plants are transmitted by B. tabaci at a similar rate. We compared the begomovirus profiles that were detected in a total of 37 whitefly populations and 52 host plants on Java Island, Indonesia. Seven begomovirus species were detected in B. tabaci at different rates: pepper yellow leaf curl Indonesia virus (PepYLCIV, 56.8%), tomato yellow leaf curl Kanchanaburi virus (TYLCKaV, 46.0%), tomato leaf curl New Delhi virus (ToLCNDV, 21.6%), squash leaf curl China virus (SLCCNV, 21.6%), ageratum yellow vein China virus (AYVCNV, 2.7%), mungbean yellow mosaic India virus (MYMIV, 2.7%), and okra enation leaf curl virus (OELCuV, 2.7%). The begomoviruses were detected at different rates in three cryptic species of B. tabaci. In addition, six begomovirus species were detected in the various host plants at different rates: PepYLCIV (67.3%), TYLCKaV (53.9%), ToLCNDV (13.5%), MYMIV (11.5%), AYVCNV (3.9%), and Tomato yellow leaf curl Thailand virus (TYLCTHV) (1.9%). By comparing the virus presence between whiteflies and plants, five begomoviruses (AYVCNV, MYMIV, PepYLCIV, ToLCNDV, and TYLCKaV) were detected in both samples, but their sequence similarity was highly variable depending on the begomovirus themselves; TYLCKaV was highest (99.4%-100%) than any other viruses. Our study suggests B. tabaci acquire begomoviruses at different rates from plants. This study provides important information on the potential variation in the begomovirus transmission mechanism.

Sida Golden Mosaic Virus, an Emerging Pathogen of Snap Bean (Phaseolus vulgaris L.) in the Southeastern United States

Sida golden mosaic virus (SiGMV) was first detected from snap bean (Phaseolus vulgaris L.) in Florida in 2006 and recently in Georgia in 2018. Since 2018, it has caused significant economic losses to snap bean growers in Georgia. This study, using a SiGMV isolate field-collected from prickly sida (Sida spinosa L.), examined the putative host range, vector-mediated transmission, and SiGMV-modulated effects on host-vector interactions. In addition, this study analyzed the phylogenetic relationships of SiGMV with other begomoviruses reported from Sida spp. Host range studies confirmed that SiGMV can infect seasonal crops and perennial weed species such as snap bean, hollyhock (Alcea rosea L.), marsh mallow (Althaea officinalis L.), okra (Abelmoschus esculentus (L.) Moench), country mallow (Sida cordifolia L.), prickly sida (S. spinosa), and tobacco (Nicotiana tabacum L.). The incidence of infection ranged from 70 to 100%. SiGMV-induced symptoms and virus accumulation varied between hosts. The vector, Bemisia tabaci Gennadius, was able to complete its life cycle on all plant species, irrespective of SiGMV infection status. However, SiGMV infection in prickly sida and country mallow positively increased the fitness of whiteflies, whereas SiGMV infection in okra negatively influenced whitefly fitness. Whiteflies efficiently back-transmitted SiGMV from infected prickly sida, hollyhock, marsh mallow, and okra to snap bean, and the incidence of infection ranged from 27 to 80%. Complete DNA-A sequence from this study shared 97% identity with SiGMV sequences reported from Florida and it was determined to be closely related with sida viruses reported from the New World. These results suggest that SiGMV, a New World begomovirus, has a broad host range that would allow its establishment in the farmscapes/landscapes of the southeastern United States and is an emerging threat to snap bean and possibly other crops.

Antagonism of tomato spotted wilt virus against tomato yellow leaf curl virus in Nicotiana benthamiana detected by transcriptome analysis

BACKGROUND

Tomato spot wilt virus (TSWV) and tomato yellow leaf curl virus (TYLCV) are highly harmful viruses in agricultural production, which can cause serious economic losses to crops and even devastating consequences for vegetable yield in some countries and regions. Although the two viruses belong to different families and have different transmission vectors, they share most hosts.

OBJECTIVE

This study aimed to examine the transcriptomic expression of single and mixed inoculations of TSWV and TYLCV, leading to antagonism using high-throughput RNA sequencing.

METHODS

We confirmed the single and mixed infections of these viruses in Nicotiana benthamiana (N. benthamiana) by artificial inoculation. And the expression changes of related genes and their biological functions and pathways during the mixed infection of TSWV and TYLCV were analyzed by comparative transcriptome.

RESULTS

Basically, similar symptoms were observed in the plants singly infected with TSWV and co-infected with TYLCV; the symptoms of TYLCV in the co-infected plants were not obvious compared with single TYLCV infections. When inoculated with TYLCV, the accumulation of the virus significantly reduced in single and mixed infections with TSWV; the TSWV accumulated slightly less in co-infection with TYLCV, whereas this reduction was much smaller than that of TYLCV. The results suggested that TSWV had an antagonistic effect on the accumulation of TYLCV in N. benthamiana. It mainly focused on the changes in unique differentially expressed genes (DEGs) caused by the co-infection of TSWV and TYLCV. The eight pathways enriched by upregulated DEGs mainly included amino acid biosynthesis, citrate cycle (or tricarboxylic acid cycle, TCA cycle), and so on. However, only pentose phosphate pathway (PPP) and peptidoglycan biosynthesis could be downregulated in the Kyoto Encyclopedia of Genes and Genomes pathway in which peptidoglycan biosynthesis was involved in upregulated and downregulated pathways.

CONCLUSIONS

The antagonistic effect of TSWV on TYLCV in N.benthamiana and the change trends and specific pathways of DEGs in this process were found. Our study provided new insights into the host regulation and competition between viruses in response to TSWV and TYLCV mixed infection.

Updates on cowpea viruses in Southwest Nigeria: distribution, prevalence and coinfection

Cowpea is an important source of dietary proteins in the semi-arid regions of sub-Saharan Africa. Its productivity is constrained by several viral diseases and there are limited updates on the incidence and distribution of these diseases in Nigeria. This study assessed the distribution and prevalence of cowpea viruses in Southwest Nigeria. Field surveys were conducted in 2017 and 2018, in which a total of 600 leaf samples were randomly collected from 60 cowpea fields in four (Oyo, Ogun, Ondo and Osun) states at 15 fields per state and 10 samples per field. Disease incidence and severity were recorded while virus infections were confirmed by enzyme-linked immunosorbent assay or reverse transcription polymerase chain reaction. Viral disease symptoms of systemic mosaic, mottling, puckering, vein-banding, leaf deformation and stunted growth were observed. Highest virus incidence and severity (100% and 4.8 ± 0.4) were observed at Adeosun Avenue, Ondo state, whereas Boredun, Osun state had the least (80% and 3.8 ± 0.7), with some symptomless fields found among the states. Seven viruses, viz.: cowpea aphid-borne mosaic virus (CABMV), cowpea mild mottle virus (CPMMV), bean common mosaic virus-blackeye cowpea mosaic strain (BCMV-BlCM), cucumber mosaic virus (CMV), southern bean mosaic virus (SBMV), cowpea mottle virus (CMoV) and cowpea yellow mosaic virus (CYMV) were detected from 173 (28.8%) samples collected from 32 (53.3%) fields across the states. CPMMV was prevalent, detected from 30.0% of surveyed fields, whereas CYMV was the least prevalent (3.3%). Multiple infections of two to four viruses were observed among 12.5% of samples from 51.7% of fields. Highest incidence of single and multiple virus infections were observed in Ondo state. This updates on virus distributions in Southwest Nigeria will be useful for multiple virus resistance-breeding programs and other viral disease management strategies for improved cowpea productivity.

Supplementary Information

The online version contains supplementary material available at 10.1007/s42360-022-00576-8.

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.

PepYLCIV and PepYLCAV resistance gene Pepy-2 encodes DFDGD-Class RNA-dependent RNA polymerase in Capsicum

A begomovirus resistance gene Pepy-2 encoding the DFDGD-Class RNA-dependent RNA polymerase 3a was identified in pepper (C. annuum) through the forward and reverse genetic analyses. In several countries throughout the world, the whitefly-transmitted begomovirus causes massive yield losses in pepper (Capsicum spp.) production. Although introgression of the genetic resistance against begomovirus to commercial cultivars is strongly required, the recently discovered recessive resistance gene pepy-1, which encodes the messenger RNA surveillance factor Pelota, is the only begomovirus resistance gene identified in Capsicum so far. In this study, we fine-mapped another begomovirus resistance gene from PG1-1 (C. annuum), which is resistant to pepper yellow leaf curl Indonesia virus (PepYLCIV) and pepper yellow leaf curl Aceh virus (PepYLCAV), to further speed up the marker-assisted breeding of begomovirus resistance in peppers. A single dominant locus, Pepy-2, conferring resistance against PepYLCIV in PG1-1 was identified on chromosome 7 by screening recombinants from the F₂ and F₃ segregating populations derived from a cross between PG1-1 and begomovirus susceptible SCM334. In the target region spanning 722 kb, a strong candidate gene, the RNA-dependent RNA polymerase 3a (CaRDR3a), was identified. The whole-genome and transcriptome sequences of PG1-1 and SCM334 revealed a single Guanine (G) deletion in CaRDR3a first exon, causing a frameshift resulting in loss-of-function in SCM334. In addition, multiple loss-of-function alleles of CaRDR3a were identified in the reference sequences of C. annuum, C. chinense, and C. baccatum in the public database. Furthermore, virus-induced gene silencing of CaRDR3a in PG1-1 resulted in the loss of resistance against PepYLCIV. PG1-1 and the DNA marker developed in this study will be useful to breeders using Pepy-2 in their breeding programs.

Impact of viral silencing suppressors on plant viral synergism: a global agro-economic concern

Plant viruses are known for their devastating impact on global agriculture. These intracellular biotrophic pathogens can infect a wide variety of plant hosts all over the world. The synergistic association of plant viruses makes the situation more alarming. It usually promotes the replication, movement, and transmission of either or both the coexisting synergistic viral partners. Although plants elicit a robust antiviral immune reaction, including gene silencing, to limit these infamous invaders, viruses counter it by encoding viral suppressors of RNA silencing (VSRs). Growing evidence also suggests that VSRs play a driving role in mediating the plant viral synergism. This review briefly discusses the evil impacts of mixed infections, especially synergism, and then comprehensively describes the emerging roles of VSRs in mediating the synergistic association of plant viruses. KEY POINTS: • Synergistic associations of plant viruses have devastating impacts on global agriculture. • Viral suppressors of RNA silencing (VSRs) play key roles in driving plant viral synergism.

Capsicum-infecting begomoviruses as global pathogens: host-virus interplay, pathogenesis, and management

Whitefly-transmitted begomoviruses are among the major threats to the cultivation of Capsicum spp. (Family: Solanaceae) worldwide. Capsicum-infecting begomoviruses (CIBs) have a broad host range and are commonly found in mixed infections, which, in turn, fuels the emergence of better-adapted species through intraspecies and interspecies recombination. Virus-encoded proteins hijack host factors to breach the well-coordinated antiviral response of plants. Epigenetic modifications of histones associated with viral minichromosomes play a critical role in this molecular arms race. Moreover, the association of DNA satellites further enhances the virulence of CIBs as the subviral agents aid the helper viruses to circumvent plant antiviral defense and facilitate expansion of their host range and disease development. The objective of this review is to provide a comprehensive overview on various aspects of CIBs such as their emergence, epidemiology, mechanism of pathogenesis, and the management protocols being employed for combating them.

Coinfection by Two Begomoviruses Aggravates Plant Symptoms But Does Not Influence the Performance and Preference of Insect Vector Bemisia tabaci (Hemiptera: Aleyrodidae)

In nature, a plant can be infected by multiple viruses simultaneously. However, the effects of coinfection on plant-vector interactions are less well studied. Two begomoviruses of the family Geminiviridae, Tomato yellow leaf curl virus (TYLCV) and Tomato yellow leaf curl China virus (TYLCCNV), occur sympatrically in China. Each of them is reported to increase the performance of whitefly vector via manipulation of plant traits. In this study, we examined the effects of coinfection by the two viruses TYLCV and TYLCCNV on plant-whitefly interactions, compared to that infected by a single virus. We found that plants infected by two viruses showed aggravated symptoms but the performance and preference of whiteflies were not altered significantly compared to singly-infected plants. Coinfection suppressed the transcription of genes involved in jasmonic acid (JA) signaling pathway in plants, but showed no significant difference to single-virus infected plants. These findings suggest that although TYLCV and TYLCCNV may synergistically induce plant symptoms, they did not manipulate synergistically plant-mediated responses to the insect vector.

Viral Interactions and Pathogenesis during Multiple Viral Infections in Agaricus bisporus

Viral interactions during multiple viral infections were examined in Agaricus bisporus cultures harboring 9 viruses (comprising 18 distinct viral RNAs) by statistically analyzing their relative abundance in fruitbodies. Four clusters of viral RNA were identified that suggested synergism and coreplication. Pairwise correlations revealed negative and positive correlations between clusters, indicating further synergisms and an antagonism involving a group containing a putative hypovirus and four nonhost ORFan RNAs (RNAs with no similarity to known sequences) possibly acting as defective interfering RNAs. The disease phenotype was observed in 10 to 15% of the fruitbodies apparently randomly located among asymptomatic fruitbodies. The degree of symptom expression consistently correlated with the levels of the multipartite virus AbV16. Diseased fruitbodies contained very high levels of AbV16 and AbV6 RNA2; these levels were orders of magnitude higher than those in asymptomatic tissues and were shown statistically to be discretely higher populations of abundance, indicating an exponential shift in the replicative capacity of the virus. High levels of AbV16 replication were specific to the fruitbody and not found in the underlying mycelium. There appeared to be a stochastic element occurring in these viral interactions, as observed in the distribution of diseased symptoms across a culture, differences in variance between experiments, and a number of additional viruses undergoing the step-jump in levels between experiments. Possible mechanisms for these multiple and simultaneous viral interactions in single culture are discussed in relation to known virus-host regulatory mechanisms for viral replication and whether additional factors could be considered to account for the 1,000-fold increase in AbV16 and AbV6 RNA2 levels.

Role of viral suppressors governing asymmetric synergism between tomato-infecting begomoviruses

Mixed viral infections are common in fields and frequently exacerbate disease severity via synergistic interactions among individual viral genomic components leading to major crop loss. Two predominant species of tomato-infecting begomoviruses, Tomato leaf curl New Delhi virus (ToLCNDV) and Tomato leaf curl Gujarat virus (ToLCGuV), are known to cause severe leaf curl disease of tomato in India. Previously, we have demonstrated asymmetric synergism between these two distinct begomovirus species during mixed infection in solanaceous hosts. In the present study, we have identified the underlying proteins that positively regulate asymmetric synergism and their effect on plant defense machinery. During co-infection, the AC2 and AV2 of ToLCGuV enhanced ToLCNDV DNA accumulation in Nicotiana benthamiana as well as in their natural host, tomato. Furthermore, we found that AC2 and AV2 of ToLCNDV and AV2 of ToLCGuV play a critical role in suppression of post transcriptional gene silencing (PTGS) machinery. Taken together, AC2 and AV2 encoded proteins of ToLCGuV are the crucial viral factors promoting asymmetric synergism with ToLCNDV. KEY POINTS: • Begomoviral suppressors play vital roles in viral synergism. • AC2 and AV2 of ToLCGuV asymmetrically enhance ToLCNDV accumulation. • AC2 and AV2 of ToLCNDV and ToLCGuV AV2 are major PTGS suppressors.

Identification and Characterization of Two Novel Geminiviruses Associated with Paper Mulberry (Broussonetia papyrifera) Leaf Curl Disease

Paper mulberry (Broussonetia papyrifera) is a perennial woody plant used as source material for Cai Lun paper making, in traditional Chinese medicine, and as livestock feed. To identify the presence of viruses in paper mulberry plants affected by a disease with leaf curl symptoms, high-throughput sequencing of total RNA was performed. Analysis of transcriptome libraries allowed the reconstruction of two geminivirus-like genomes. Rolling-circle amplification and PCR with back-to-back primers confirmed the presence of two geminiviruses with monopartite genomes in these plants, with the names paper mulberry leaf curl virus 1 and 2 (PMLCV-1 and PMLCV-2) proposed. The genomes of PMLCV-1 (3,056 nt) and PMLCV-2 (3,757 to 3,763 nt) encode six proteins, with the V4 protein of PMLCV-1 and the V3 proteins of both viruses having low similarities to any known protein in databases. Alternative splicing of an intron, akin to that of mastre-, becurto-, capula-, and grabloviruses, was identified by small RNA (sRNA)-seq and RNA-seq reads mapping to PMLCV-1 and PMLCV-2 antisense transcripts. Phylogenetic analyses and pairwise comparisons showed that PMLCV-1 and PMLCV-2 are most closely related to, but distinct from, two unassigned geminiviruses, citrus chlorotic dwarf associated virus and mulberry mosaic dwarf associated virus, suggesting that they are two new members of the family Geminiviridae. Field investigation confirmed the close association of the two viruses with leaf curl symptoms in paper mulberry plants and that coinfection can aggravate the symptoms.

Biology and Interaction of the Natural Occurrence of Distinct Monopartite Begomoviruses Associated With Satellites in Capsicum annum From India

Chili (Capsicum annuum L.) is an important vegetable and spice crop of tropical and sub-tropical regions. Chili plants showing upward leaf curling, leaf crinkling, and leaf yellowing symptoms, collected from Sikar district of Rajasthan, India, were found to be associated with begomovirus and satellite molecules. The presence of virus was confirmed by PCR using virus-specific primer. The full-length genomic DNA-A of three begomovirus (MM-1, CS-1 and RV-1) and two satellites (MM-2 and MM-3) were cloned which was identified from single symptomatic chili plant. The genome organization of isolated three viruses is similar to those of other Old World monopartite begomoviruses. The comparison of the sequences and closest phylogenetic relationships for the begomoviruses, betasatellite and alphasatellite DNAs revealed that MM-1 was designated as DNA-A of Chili leaf curl virus (ChiLCV), CS-1 is considered to be a new distinct species of Tomato leaf curl Gujrat virus (ToLCGV) whereas RV-1 as a new strain of Cotton leaf curl Multan virus (CLCuMuV). The DNA-A component of ChiLCV showed 8.6%, ToLCGV of 16.6% and CLCuMuV of 7.7% average evolutionary divergence, concomitantly, the betasatellite and alphasatellite molecule had 9.9% and 5.9% overall sequence divergence, respectively. Interestingly, most of the begomoviruses were found to be intra-species recombinants. The dN/dS ratio and Tajima D value of all viral DNA-A component and their associated betasatellite showed their selective control on evolutionary relationships. The nucleotide substitution rates were determined for the DNA-A genomes of ChiLCV (7.22 × 10^–4 substitutions site^–1 year^–1), CLCuMuV (1.49 × 10^–4 substitutions site^–1 year^–1), ToLCGV (7.47 × 10^–4 substitutions site^–1 year^–1), the genome of associated ChiLCB (4.20 × 10^–4 substitutions site^–1 year^–1) and CLCuMuA (1.49 × 10^–4 substitutions site^–1 year^–1). Agro-inoculation studies indicate that the presence of DNA betasatellite induce severe symptoms in N. benthamiana and chili, suggesting prerequisite association for typical disease development.

First report of begomoviruses infecting Cucumis sativus L. in North America and identification of a proposed new begomovirus species

Background

Members of the Begomovirus genus are phytopathogens that infect dicotyledonous plants, producing economic losses in tropical and subtropical regions. To date, only seven species of begomoviruses (BGVs) infecting cucumber have been described. Most cucumber infections were reported in South Asia. In the Americas, begomoviral infections affecting cucumber are scarce; just one report of begomovirus has been described in South America. The presence of whitefly and typical symptoms of viral infections observed in a cucumber field in Colima, Mexico, suggested that plants in this field were affected by BGVs.

Methods

To identify the BGVs infecting cucumber, we performed a high-throughput sequencing and compared the assembled contigs against the GenBank nucleic acid sequence database. To confirm the presence of viruses in cucumber samples, we performed a PCR detection using specific oligonucleotides. We cloned and sequenced by Sanger method the complete genome of a potential new begomovirus. Begomovirus species demarcation was performed according to the International Committee on Taxonomy of Viruses. The evolutionary relationship of the new virus was inferred using phylogenetic and recombination analyses.

Results

We identified five species of begomovirus infecting plants in a field. None of these have been previously reported infecting cucumber. One of the five species of viruses here reported is a new begomovirus species. Cucumber chlorotic leaf virus, the new species, is a bipartite begomovirus that has distinctive features of viruses belonging to the squash leaf curl virus clade.

Conclusions

The findings here described represent the first report of begomoviral infection affecting cucumber plants in North America. Previous to this report, only seven begomovirus species have been reported in the world, here we found five species infecting cucumber plants in a small sample suggesting that cucumber is vulnerable to BGVs. One of these viruses is a new species of begomovirus which is the first begomovirus originally isolated from the cucumber. The findings of this report could help to develop strategies to fight the begomoviral infections that affect cucumber crops.

Virus-virus interactions in a plant host and in a hemipteran vector: Implications for vector fitness and virus epidemics

Mixed virus infection in host plants can differentially alter the plant phenotype, influence vector fitness, and affect virus acquisition and inoculation by vectors than single-virus infection. Vector acquisition of multiple viruses from multiple host plants could also differentially affect vector fitness and virus inoculation than acquisition of one virus. Whitefly-virus pathosystems in the southern United States include both the above-stated facets. For the first facet, this study examined the effects of single and mixed infection of cucurbit leaf crumple virus (CuLCrV, a begomovirus) and cucurbit yellow stunting disorder virus (CYSDV, a crinivirus) infecting squash on whitefly (Bemisia tabaci Gennadius MEAM1) host preference and fitness. Mixed infection of CuLCrV and CYSDV in squash plants severely altered their phenotype than single infection. The CYSDV load was reduced in mixed-infected squash plants than in singly-infected plants. Consequently, whiteflies acquired reduced amounts of CYSDV from mixed-infected plants than singly-infected plants. No differences in CuLCrV load were found between singly- and mixed-infected squash plants, and acquisition of CuLCrV by whiteflies did not vary between singly- and mixed-infected squash plants. Both singly- and mixed-infected plants similarly affected whitefly preference, wherein non-viruliferous and viruliferous (CuLCrV and/or CYSDV) whiteflies preferred non-infected plants over infected plants. The fitness study involving viruliferous and non-viruliferous whiteflies revealed no differences in developmental time and fecundity. For the second facet, this study evaluated the effects of individual or combined acquisition of tomato-infecting tomato yellow leaf curl virus (TYLCV, a begomovirus) and squash-infecting CuLCrV on whitefly host preference and fitness. Whiteflies that acquired both CuLCrV and TYLCV had significantly lower CuLCrV load than whiteflies that acquired CuLCrV alone, whereas TYLCV load remained unaltered when acquired individually or in conjunction with CuLCrV. Whitefly preference was not affected following individual or combined virus acquisition. Viruliferous (CuLCrV and/or TYLCV) whiteflies preferred to settle on non-infected tomato and squash plants. The mere presence of CuLCrV and/or TYLCV in whiteflies did not affect their fitness. Taken together, these results indicate that mixed infection of viruses in host plants and acquisition of multiple viruses by the vector could have implications for virus accumulation, virus acquisition, vector preference, and epidemics that sometimes are different from single-virus infection or acquisition.

Implications of mixed viral infections on plant disease ecology and evolution

Mixed viral infections occur more commonly than would be expected by chance in nature. Virus-virus interactions may affect viral traits and leave a genetic signature in the population, and thus influence the prevalence and emergence of viral diseases. Understanding about how the interactions between viruses within a host shape the evolutionary dynamics of the viral populations is needed for viral disease prevention and management. Here, we first synthesize concepts implied in the occurrence of virus-virus interactions. Second, we consider the role of the within-host interactions of virus-virus and virus-other pathogenic microbes, on the composition and structure of viral populations. Third, we contemplate whether mixed viral infections can create opportunities for the generation and maintenance of viral genetic diversity. Fourth, we attempt to summarize the evolutionary response of viral populations to mixed infections to understand how they shape the spatio-temporal dynamics of viral populations at the individual plant and field scales. Finally, we anticipate the future research under the reconciliation of molecular epidemiology and evolutionary ecology, drawing attention to the need of adding more complexity to future research in order to gain a better understanding about the mechanisms operating in nature.

Superinfection by PHYVV Alters the Recovery Process in PepGMV-Infected Pepper Plants

Geminiviruses are important plant pathogens that affect crops around the world. In some geminivirus-host interactions, infected plants show recovery, a phenomenon characterized by symptom disappearance in newly emerging leaves. In pepper-Pepper golden mosaic virus (PepGMV) interaction, the host recovery process involves a silencing mechanism that includes both post-transcriptional (PTGS) and transcriptional (TGS) gene silencing pathways. Under field conditions, PepGMV is frequently found in mixed infections with Pepper huasteco yellow vein virus (PHYVV), another bipartite begomovirus. Mixed infected plants generally show a synergetic phenomenon and do not present recovery. Little is known about the molecular mechanism of this interaction. In the present study, we explored the effect of superinfection by PHYVV on a PepGMV-infected pepper plant showing recovery. Superinfection with PHYVV led to (a) the appearance of severe symptoms, (b) an increase of the levels of PepGMV DNA accumulation, (c) a decrease of the relative methylation levels of PepGMV DNA, and (d) an increase of chromatin activation marks present in viral minichromosomes. Finally, using heterologous expression and silencing suppression reporter systems, we found that PHYVV REn presents TGS silencing suppressor activity, whereas similar experiments suggest that Rep might be involved in suppressing PTGS.

When Viruses Play Team Sports: Mixed Infections in Plants

The pathological importance of mixed viral infections in plants might be underestimated except for a few well-characterized synergistic combinations in certain crops. Considering that the host ranges of many viruses often overlap and that most plant species can be infected by several unrelated viruses, it is not surprising to find more than one virus simultaneously in the same plant. Furthermore, dispersal of the majority of plant viruses relies on efficient transmission mechanisms mediated by vector organisms, mainly but not exclusively insects, which can contribute to the occurrence of multiple infections in the same plant. Recent work using different experimental approaches has shown that mixed viral infections can be remarkably frequent, up to the point that they could be considered the rule more than the exception. The purpose of this review is to describe the impact of multiple infections not only on the participating viruses themselves but also on their vectors and on the common host. From this standpoint, mixed infections arise as complex events that involve several cross-interacting players, and they consequently require a more general perspective than the analysis of single-virus/single-host approaches for a full understanding of their relevance.

Incidence of viruses infecting pepper in Thailand

This study was conducted to determine the incidence, diversity and distribution of viruses infecting pepper (Capsicum spp.) in the central, northern and northeastern parts of Thailand. During a survey in 2016 - 2019, a total of 2,149 leaf samples from symptomatic and asymptomatic peppers were collected randomly from farmer's fields, and preliminary tested by an enzyme-linked immunosorbent assay (ELISA) using 7 antibodies specific for cucumber mosaic virus (CMV), chilli veinal mottle virus (ChiVMV), tomato necrotic ringspot virus (TNRV), tobacco mosaic virus (TMV), potato virus Y (PVY), tomato spotted wilt virus (TSWV), and begomoviruses. Our data revealed that the incidence of the viruses infecting pepper in Thailand was high, accounting for nearly 70% (1,482 infected samples). The highest viral incidence was found in the central part (96%), followed by the north (74.4%) and the northeastern (52.8%), respectively. Begomoviruses, CMV, ChiVMV, and TNRV were detected in the samples at varying rates, whereas PVY, TMV, and TSWV were not detected. Of these, the most frequently found virus was Begomoviruses accounting for nearly 33%, with the highest rate (ca. 82%) in the central Provinces of Thailand. In addition, of the 1,482 infected samples, mixed infections among the four viruses were also found in 616 samples (ca. 42%), and CMV + ChiVMV (approximately 11%) was the most common mixed infection. This is the first report describing an occurrence of viruses in pepper of Thailand, and the results obtained have revealed that viruses infecting pepper are widespread, which may pose a threat to pepper production in Thailand.

Detection of disease in Cucurbita maxima Duch. ex Lam. caused by a mixed infection of Zucchini yellow mosaic virus, Watermelon mosaic virus, and Cucumber mosaic virus in Southeast China using a novel small RNA sequencing method

The genus Cucurbita comprises many popular vegetable and ornamental plants, including pumpkins, squashes, and gourds, that are highly valued in China as well as in many other countries. During a survey conducted in Zhejiang province, Southeast China in 2016, severe symptoms of viral infection were observed on Cucurbita maxima Duch. ex Lam. Diseased plants showed symptoms such as stunting, mosaicking, Shoe string, blistering, yellowing, leaf deformation, and fruit distortion. Approximately, 50% of Cucurbita crops produced in Jinhua were diseased, causing an estimated yield loss of 35%. In this study, we developed a method using all known virus genomes from the NCBI database as a reference to map small RNAs to develop a diagnostic tool that could be used to diagnose virus diseases of C. maxima. 25 leaf samples from different symptomatic plants and 25 leaf samples from non-symptomatic plants were collected from the experimental field of Jihua National Agricultural Technology Garden for pathogen identification. Small RNAs from each set of three symptomatic and non-symptomatic samples were extracted and sequenced by Illumina sequencing. Twenty-four different viruses were detected in total. However, the majority of the small RNAs were from Zucchini yellow mosaic virus (ZYMV), Watermelon mosaic virus (WMV), and Cucumber mosaic virus (CMV). Mixed infections of these three viruses were diagnosed in leaf samples from diseased plants and confirmed by reverse transcription PCR (RT-PCR) using primers specific to these three viruses. Crude sap extract from symptomatic leaf samples was mechanically inoculated back into healthy C. maxima plants growing under greenhouse conditions. Inoculated plants developed the same disease symptoms as those observed in the diseased plants and a mixed infection of ZYMV, WMV, and CMV was detected again by RT-PCR, thus fulfilling Koch's postulates. The diagnostic method developed in this study involves fewer bioinformatics processes than other diagnostic methods, does not require complex settings for bioinformatics parameters, provides a high level of sensitivity to rapidly diagnose plant samples with symptoms of virus diseases and can be performed cheaply. This method therefore has the potential to be widely applied as a diagnostic tool for viruses that have genome information in the NCBI database.

Genome of a known but distinct begomovirus associated with a novel satellite molecule infecting a new host bitter gourd (Momordica charantia)

Coccinia mosaic Virdhunagar virus (KY860899), Tomato leaf curl New Delhi virus (KY860898) and Tomato leaf curl Virdhunagar alphasatellite (KY848691) were found to be associated with leaf curl disease in Momordica charantia (bitter gourd). The complete nucleotide sequence of Coccinia mosaic Virdhunagar virus showed 82% identity with Coccinia mosaic Tamil Nadu virus (KM244719), whereas Tomato leaf curl New Delhi virus was 96% identical to Tomato leaf curl New Delhi virus (KP868764) and Tomato leaf curl Virdhunagar alphasatellite illustrated 81% similarity with Tomato leaf curl New Delhi alphasatellite (JQ041697). Phylogenetic and RDP analysis revealed the proximity of these begomoviruses with other monopartite begomoviruses and alphasatellites already reported from India. As per the threshold criteria laid down by International Committee on Taxonomy of Viruses for species demarcation in begomoviruses and satellite molecules, the identified virus isolates, Coccinia mosaic Virdhunagar virus and Tomato leaf curl Virdhunagar alphasatellite are proposed as new species. To the best of our knowledge, this is the first ever account of mixed infection of begomoviruses in Momordica charantia, a vegetable crop commonly cultivated throughout India.

Co-infection with a wheat rhabdovirus causes a reduction in Mal de Río Cuarto virus titer in its planthopper vector

Mal de Río Cuarto virus (MRCV, Fijivirus, Reoviridae) causes one of the most important diseases in maize (Zea mays L.) in Argentina and has been detected in mixed infections with a rhabdovirus closely related to Maize yellow striate virus. In nature both viruses are able to infect maize and several grasses including wheat, and are transmitted in a persistent propagative manner by Delphacodes kuscheli Fennah (Hemiptera: Delphacidae). This work describes the interactions between MRCV and rhabdovirus within their natural vector and the consequences of such co-infection regarding virus transmission and symptom expression. First- and third-instar D. kuscheli nymphs were fed on MRCV-infected wheat plants or MRCV-rhabdovirus-infected oat plants, and two latency periods were considered. Transmission efficiency and viral load of MRCV-transmitting and non-transmitting planthoppers were determined by real-time quantitative polymerase chain reaction analysis (RTqPCR). Vector transmission efficiency was related to treatments (life stages at acquisition and latency periods). Nevertheless, no correlation between transmission efficiency and type of inoculum used to infect insects with MRCV was found. Treatment by third-instar nymphs 17 days after Acquisition Access Period was the most efficient for MRCV transmission, regardless of the type of inoculum. Plants co-infected with MRCV and rhabdovirus showed the typical MRCV symptoms earlier than plants singly infected with MRCV. The transmitting planthoppers showed significantly higher MRCV titers than non-transmitting insects fed on single or mixed inocula, confirming that successful MRCV transmission is positively associated with viral accumulation in the insect. Furthermore, MRCV viral titers were higher in transmitting planthoppers that acquired this virus from a single inoculum than in those that acquired the virus from a mixed inoculum, indicating that the presence of the rhabdovirus somehow impaired MRCV replication and/or acquisition. This is the first study about interactions between MRCV and a rhabdovirus closely related to Maize yellow striate virus in this insect vector (D. kuscheli), and contributes to a better understanding of planthopper-virus interactions and their epidemiological implications.

Coinfection Timing Drives Host Population Dynamics through Changes in Virulence

Infections of one host by multiple parasites are common, and several studies have found that the order of parasite invasion can affect both within-host competition and disease severity. However, it is unclear to what extent coinfection timing might be important to consider when modeling parasite impacts on host populations. Using a model system of two viruses infecting barley, we found that simultaneous infections of the two viruses were significantly more damaging to hosts than sequential coinfections. While priority effects were evident in within-host concentrations of sequential coinfections, priority did not influence any parameters (such as virulence or transmission rate) that affect host population dynamics. We built a susceptible-infected model to examine whether the observed difference in coinfection virulence could impact host population dynamics under a range of scenarios. We found that coinfection timing can have an important but context-dependent effect on projected host population dynamics. Studies that examine only simultaneous coinfections could inflate disease impact predictions.

RNAi-derived transgenic resistance to Mungbean yellow mosaic India virus in cowpea

Cowpea is an important grain legume crop of Africa, Latin America, and Southeast Asia. Leaf curl and golden mosaic diseases caused by Mungbean yellow mosaic India virus (MYMIV) have emerged as most devastating viral diseases of cowpea in Southeast Asia. In this study, we employed RNA interference (RNAi) strategy to control cowpea-infecting MYMIV. For this, we generated transgenic cowpea plants harbouring three different intron hairpin RNAi constructs, containing the AC2, AC4 and fusion of AC2 and AC4 (AC2+AC4) of seven cowpea-infecting begomoviruses. The T₀ and T₁ transgenic cowpea lines of all the three constructs accumulated transgene-specific siRNAs. Transgenic plants were further assayed up to T₁ generations, for resistance to MYMIV using agro-infectious clones. Nearly 100% resistance against MYMIV infection was observed in transgenic lines, expressing AC2-hp and AC2+AC4-hp RNA, when compared with untransformed controls and plants transformed with empty vectors, which developed severe viral disease symptoms within 3 weeks. The AC4-hp RNA expressing lines displayed appearance of milder symptoms after 5 weeks of MYMIV-inoculation. Northern blots revealed a positive correlation between the level of transgene-specific siRNAs accumulation and virus resistance. The MYMIV-resistant transgenic lines accumulated nearly zero or very low titres of viral DNA. The transgenic cowpea plants had normal phenotype with no yield penalty in greenhouse conditions. This is the first demonstration of RNAi-derived resistance to MYMIV in cowpea.

The pepper virome: natural co-infection of diverse viruses and their quasispecies

BACKGROUND

The co-infection of diverse viruses in a host plant is common; however, little is known about viral populations and their quasispecies in the host.

RESULTS

Here, we report the first pepper viromes that were co-infected by different types of viral genomes. The pepper viromes are dominated by geminivirus DNA-A followed by a novel carlavirus referred to as Pepper virus A. The two pepper cultivars share similar viral populations and replications. However, the quasispecies for double-stranded RNA virus and two satellite DNAs were heterogeneous and homogenous in susceptible and resistant cultivars, respectively, indicating the quasispecies of an individual virus depends on the host.

CONCLUSIONS

Taken together, we provide the first evidence that the host plant resistant to viruses has an unrevealed antiviral system, affecting viral quasispecies, not replication.

Synergies and antagonisms in virus interactions

Metagenomic surveys and data from next generation sequencing revealed that mixed infections among plant viruses are probably a rule rather than an exception in natural pathosystems. The documented cases may range from synergism to antagonism, which may depend from the spatiotemporal order of arrival of the viruses on the host and upon the host itself. In synergistic interactions, the measurable differences in replication, phenotypic and cytopathological changes, cellular tropism, within host movement, and transmission rate of one of the two viruses or both are increased. Conversely, a decrease in replication, or inhibition of one or more of the above functions by one virus against the other, leads to an antagonistic interaction. Viruses may interact directly and by transcomplementation of defective functions or indirectly, through responses mediated by the host like the defense mechanism based on RNA silencing. Outcomes of these interactions can be applied to the risk assessment of transgenic crops expressing viral proteins, or cross-protected crops for the identification of potential hazards. Prior to experimental evidence, mathematical models may help in forecasting challenges deriving from the great variety of pathways of synergistic and antagonistic interactions. Actually, it seems that such predictions do not receive sufficient credit in the framework of agriculture.

Survey, Molecular Detection, and Characterization of Geminiviruses Associated with Cassava Mosaic Disease in Zambia

A survey was conducted from April to May 2014 in 214 farmers' fields located across six major cassava-producing provinces (Western, Northwestern, Northern, Luapula, Lusaka, and Eastern) of Zambia to determine the status of cassava mosaic disease (CMD) and the species diversity of associated cassava mosaic geminiviruses (CMG). Mean CMD incidence varied across all six provinces but was greatest in Lusaka Province (81%) and least in Northern Province (44%). Mean CMD severity varied slightly between provinces, ranging from 2.78 in Eastern Province to 3.00 in Northwestern Province. Polymerase chain reaction discrimination of 226 survey samples, coupled with complete DNA-A genome sequence analysis, revealed the presence of African cassava mosaic virus (ACMV), East African cassava mosaic virus (EACMV), and East African cassava mosaic Malawi virus (EACMMV) as single or mixed infections of different proportions. Single-virus infections were predominant, occurring in 62.8% (ACMV), 5.8% (EACMMV), and 2.2% (EACMV) of samples relative to mixed-virus infections, which occurred in 19.5% (ACMV + EACMMV), 0.4% (ACMV + EACMV), and 0.9% (ACMV + EACMV + EACMMV) of samples. Phylogenetic analysis revealed the segregation of virus isolates from Zambia into clades specific to ACMV, EACMV, and EACMMV, further confirming the presence of all three viruses in Zambia. The results point to a greater diversity of CMG across major cassava-growing provinces of Zambia and implicate contaminated cassava cuttings in disease spread.

Molecular characterization and construction of an infectious clone of a pepper isolate of Beet curly top Iran virus

Geminiviruses cause curly top disease, in dicotyledonous plants which constrains host crop production. Beet curly top Iran virus (BCTIV) is a widespread Becurtovirus (family Geminiviridae) in numerous areas within Iran. In this study, we isolated and analyzed a full-length genomic DNA of a new variant of BCTIV from pepper crops in the Kaftark region, east of Shiraz (proposed acronym: BCTIV-Kaf [IR: Kaf:2016:Pepper]). Infected pepper plants showed shortening of internodes, severe interveinal chlorosis, upward leaf rolling and leaf curling. Sequence and phylogenetic analysis showed this BCTIV variant grouped with sugar beet isolates of BCTIV and has the highest similarity to a sugar beet BCTIV isolate from Negar town in Kerman province, Iran. It was more distantly related to a bean isolate of BCTIV from northeast region of Iran. A tandem repeat partial dimmer of BCTIV was constructed and found to be infectious in pepper, tomato and Nicotiana benthamiana plants. Results of this study indicated that BCTIV-Kaf is a new variant of BCTIV infecting pepper plants in Shiraz and that geographic location rather than the type of host plant has more effect on genetic diversity of BCTIV in Iran.

Synergistic interaction among begomoviruses leads to the suppression of host defense-related gene expression and breakdown of resistance in chilli

Chilli (Capsicum sp.) is one of the economically important spice and vegetable crops grown in India and suffers great losses due to the infection of begomoviruses. Conventional breeding approaches have resulted in development of a few cultivars of chilli resistant to begomoviruses. A severe leaf curl disease was observed on one such resistant chilli cultivar (Capsicum annuum cv. Kalyanpur Chanchal) grown in the experimental field of the Jawaharlal Nehru University, New Delhi. Four different viral genomic components namely, Chilli leaf curl virus (DNA A), Tomato leaf curl Bangladesh betasatellite (DNA β), Tomato leaf curl New Delhi virus (DNA A), and Tomato leaf curl Gujarat virus (DNA B) were associated with the severe leaf curl disease. Further, frequent association of these four genomic components was also observed in symptomatic plants of other chilli cultivars (Capsicum annuum cv. Kashi Anmol and Capsicum chinense cv. Bhut Jolokia) grown in the experimental field. Interaction studies among the isolated viral components revealed that Nicotiana benthamiana and chilli plants inoculated with four genomic components of begomoviruses exhibited severe leaf curl disease symptoms. In addition, this synergistic interaction resulted in increased viral DNA accumulation in infected plants. Resistant chilli plants co-inoculated with four genomic components of begomoviruses showed drastic reduction of host basal (ascorbate peroxidase, thionin, polyphenol oxidase) and specific defense-related gene (NBS-LRR) expression. Our results suggested that synergistic interaction among begomoviruses created permissive cellular environment in the resistant chilli plants which leads to breakdown of natural resistance, a phenomenon observed for the first time in chilli.

Two Populations of Viral Minichromosomes Are Present in a Geminivirus-Infected Plant Showing Symptom Remission (Recovery)

Geminiviruses are important plant pathogens characterized by circular, single-stranded DNA (ssDNA) genomes. However, in the nuclei of infected cells, viral double-stranded DNA (dsDNA) associates with host histones to form a minichromosome. In phloem-limited geminiviruses, the characterization of viral minichromosomes is hindered by the low concentration of recovered complexes due to the small number of infected cells. Nevertheless, geminiviruses are both inducers and targets of the host posttranscriptional gene silencing (PTGS) and transcriptional gene silencing (TGS) machinery. We have previously characterized a "recovery" phenomenon observed in pepper plants infected with pepper golden mosaic virus (PepGMV) that is associated with a reduction of viral DNA and RNA levels, the presence of virus-related siRNAs, and an increase in the levels of viral DNA methylation. Initial micrococcal nuclease-based assays pinpointed the presence of different viral chromatin complexes in symptomatic and recovered tissues. Using the pepper-PepGMV system, we developed a methodology to obtain a viral minichromosome-enriched fraction that does not disturb the basic chromatin structural integrity, as evaluated by the detection of core histones. Using this procedure, we have further characterized two populations of viral minichromosomes in PepGMV-infected plants. After further purification using sucrose gradient sedimentation, we also observed that minichromosomes isolated from symptomatic tissue showed a relaxed conformation (based on their sedimentation rate), are associated with a chromatin activation marker (H3K4me3), and present a low level of DNA methylation. The minichromosome population obtained from recovered tissue, on the other hand, sedimented as a compact structure, is associated with a chromatin-repressive marker (H3K9me2), and presents a high level of DNA methylation.

IMPORTANCE

Viral minichromosomes have been reported in several animal and plant models. However, in the case of geminiviruses, there has been some recent discussion about the importance of this structure and the significance of the epigenetic modifications that it can undergo during the infective cycle. Major problems in this type of studies are the low concentration of these complexes in an infected plant and the asynchronicity of infected cells along the process; therefore, the complexes isolated in a given moment usually represent a mixture of cells at different infection stages. The recovery process observed in PepGMV-infected plants and the isolation procedure described here provide two distinct populations of minichromosomes that will allow a more precise characterization of the modifications of viral DNA and its host proteins associated along the infective cycle. This structure could be also an interesting model to study several processes involving plant chromatin.

Two Populations of Viral Minichromosomes Are Present in a Geminivirus-Infected Plant Showing Symptom Remission (Recovery)

Geminiviruses are important plant pathogens characterized by circular, single-stranded DNA (ssDNA) genomes. However, in the nuclei of infected cells, viral double-stranded DNA (dsDNA) associates with host histones to form a minichromosome. In phloem-limited geminiviruses, the characterization of viral minichromosomes is hindered by the low concentration of recovered complexes due to the small number of infected cells. Nevertheless, geminiviruses are both inducers and targets of the host posttranscriptional gene silencing (PTGS) and transcriptional gene silencing (TGS) machinery. We have previously characterized a "recovery" phenomenon observed in pepper plants infected with pepper golden mosaic virus (PepGMV) that is associated with a reduction of viral DNA and RNA levels, the presence of virus-related siRNAs, and an increase in the levels of viral DNA methylation. Initial micrococcal nuclease-based assays pinpointed the presence of different viral chromatin complexes in symptomatic and recovered tissues. Using the pepper-PepGMV system, we developed a methodology to obtain a viral minichromosome-enriched fraction that does not disturb the basic chromatin structural integrity, as evaluated by the detection of core histones. Using this procedure, we have further characterized two populations of viral minichromosomes in PepGMV-infected plants. After further purification using sucrose gradient sedimentation, we also observed that minichromosomes isolated from symptomatic tissue showed a relaxed conformation (based on their sedimentation rate), are associated with a chromatin activation marker (H3K4me3), and present a low level of DNA methylation. The minichromosome population obtained from recovered tissue, on the other hand, sedimented as a compact structure, is associated with a chromatin-repressive marker (H3K9me2), and presents a high level of DNA methylation.

IMPORTANCE

Viral minichromosomes have been reported in several animal and plant models. However, in the case of geminiviruses, there has been some recent discussion about the importance of this structure and the significance of the epigenetic modifications that it can undergo during the infective cycle. Major problems in this type of studies are the low concentration of these complexes in an infected plant and the asynchronicity of infected cells along the process; therefore, the complexes isolated in a given moment usually represent a mixture of cells at different infection stages. The recovery process observed in PepGMV-infected plants and the isolation procedure described here provide two distinct populations of minichromosomes that will allow a more precise characterization of the modifications of viral DNA and its host proteins associated along the infective cycle. This structure could be also an interesting model to study several processes involving plant chromatin.

Development of plants resistant to tomato geminiviruses using artificial trans-acting small interfering RNA

RNA interference (RNAi), a conserved RNA-mediated gene regulatory mechanism in eukaryotes, plays an important role in plant growth and development, and as an antiviral defence system in plants. As a counter-strategy, plant viruses encode RNAi suppressors to suppress the RNAi pathways and consequently down-regulate plant defence. In geminiviruses, the proteins AC2, AC4 and AV2 are known to act as RNAi suppressors. In this study, we have designed a gene silencing vector using the features of trans-acting small interfering RNA (tasiRNA), which is simple and can be used to target multiple genes at a time employing a single-step cloning procedure. This vector was used to target two RNAi suppressor proteins (AC2 and AC4) of the geminivirus, Tomato leaf curl New Delhi virus (ToLCNDV). The vector containing fragments of ToLCNDV AC2 and AC4 genes, on agro-infiltration, produced copious quantities of AC2 and AC4 specific siRNA in both tobacco and tomato plants. On challenge inoculation of the agro-infiltrated plants with ToLCNDV, most plants showed an absence of symptoms and low accumulation of viral DNA. Transgenic tobacco plants were raised using the AC2 and AC4 tasiRNA-generating constructs, and T1 plants, obtained from the primary transgenic plants, were tested for resistance separately against ToLCNDV and Tomato leaf curl Gujarat virus. Most plants showed an absence of symptoms and low accumulation of the corresponding viruses, the resistance being generally proportional to the amounts of siRNA produced against AC2 and AC4 genes. This is the first report of the use of artificial tasiRNA to generate resistance against an important plant virus.

Identification of siRNA generating hot spots in multiple viral suppressors to generate broad-spectrum antiviral resistance in plants

Viruses are one of the most devastating plant pathogens causing severe economic losses worldwide. RNA silencing is a robust technology to knock down the expression of specific genes. This mechanism can be exploited to generate virus resistant plants through expression of the viral derived sequences. Viruses in turn have evolved to encode suppressors of RNA silencing to combat host defense. Mixed infection of plants is of common occurrence in nature and simultaneous targeting of suppressor(s) of multiple viruses offers an effective strategy. In this study, we have in silico designed siRNAs against suppressors of the two most devastating viruses of tomato, leaf curl causing tomato begomoviruses and Cucumber mosaic virus. Three different siRNA prediction programs were used to evaluate siRNAs generating capability of each sequence and common putative candidate siRNAs were selected fulfilling the stringent parameters. Our results indicated that in the case of each suppressor a particular region of 100-150 base pairs could be source of potent siRNAs referred as hotspots. Expression of these viral hot spots as a single construct in the plants would facilitate development of transgenic plants with a high degree of broad spectrum resistance against multiple viruses.

Plant-mediated whitefly-begomovirus interactions: research progress and future prospects

Plant-mediated interactions between begomoviruses and whiteflies exert important influences on the population dynamics of vectors and the epidemiology of plant diseases. In this article, we synthesize the relevant literature to identify patterns to the interactions. We then review studies on the ecological, biochemical and molecular mechanisms underlying the interactions and finally elaborate on the most interesting issues for future research. The interactions between begomoviruses and the insect vector, the whitefly Bemisia tabaci, via their shared host plants can be mutualistic, neutral or negative. However, in contrast to a pattern of improved performance of vectors on virus-infected plants that has been observed with persistently transmitted RNA viruses, the number of cases exhibiting mutualistic, neutral or negative effects in the indirect interactions between begomoviruses and whiteflies appear evenly distributed. With regard to the mechanisms of plant-mediated positive effects on whiteflies, two case studies indicate that suppression of plant defence and/or alteration in plant nutrition as a result of virus infection can be important. Our review shows that we are only just beginning to understand the tripartite interactions between begomoviruses, whiteflies and plants. Future efforts in this area should try to expand the number and diversity of pathosystems for investigation to reveal the patterns of interactions, to investigate the molecular and biochemical mechanisms of the interactions using a multidisciplinary approach, and to examine the virus-plant-vector interactions in the field and in natural plant communities.

Biological and molecular events associated with simultaneous transmission of plant viruses by invertebrate and fungal vectors

Viruses are likely to be the most dangerous parasites of living organisms because of their widespread occurrence, possible deleterious effects on their hosts and high rates of evolution. Virus host-to-host transmission is a critical step in the virus life cycle, because it enables survival in a given environment and efficient dissemination. As hosts of plant viruses are not mobile, these pathogens have adopted diverse transmission strategies involving various vector organisms, mainly arthropods, nematodes, fungi and protists. In nature, plants are often infected with more than one virus at a time, thereby creating potential sources for vectors to acquire and transmit simultaneously two or more viruses. Simultaneous transmission can result in multiple infections of new host plants, which become subsequent potential sources of the viruses, thus enhancing the spread of the diseases caused by these pathogens. Moreover, it can contribute to the maintenance of viral genetic diversity in the host communities. However, despite its possible significance, the problem of the simultaneous transmission of plant viruses by vectors has not been investigated in detail. In this review, the current knowledge on multiple viral transmissions by aphids, whiteflies, leafhoppers, planthoppers, nematodes and fungi is outlined.